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Harold Scheraga

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Protein Folding

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Co-Publications
Name
55
Liwo, Adam
32
Vila, Jorge
29
Ripoll, Daniel
26
Welker, Ervin
23
Narayan, Mahesh
19
Oldziej, Stanislaw
18
Czaplewski, Cezary
12
Arnautova, Yelena
12
Wedemeyer, William
11
Xu, Guoqiang
9
Shin, Hang-Cheol
9
Pillardy, Jaroslaw
9
Montelione, Gaetano
9
Khalili, Mey
8
Jagielska, Anna

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Publications

TOP 3
Vila Jorge A; Arnautova Yelena A; Martin Osvaldo A; Scheraga Harold A
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
Vila Jorge A; Scheraga Harold A
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.
Arnautova Yelena A; Vorobjev Yury N; Vila Jorge A; Scheraga Harold A
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

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All Publications

2009: Vila Jorge A; Arnautova Yelena A; Martin Osvaldo A; Scheraga Harold A
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(40):16972-7.
2009: Vila Jorge A; Scheraga Harold A
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.
Accounts of chemical research 2009;42(10):1545-53.
2009: Arnautova Yelena A; Vorobjev Yury N; Vila Jorge A; Scheraga Harold A
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.
Proteins 2009;77(1):38-51.
2009: He Yi; Xiao Yi; Liwo Adam; Scheraga Harold A
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
Journal of computational chemistry 2009;30(13):2127-35.
2009: Sobolewski Emil; Makowski Mariusz; Oldziej Stanislaw; Czaplewski Cezary; Liwo Adam; Scheraga Harold A
Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.
Protein engineering, design & selection : PEDS 2009;22(9):547-52.
2009: Skwierawska Agnieszka; Zmudzinska Wioletta; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation.
Proteins 2009;76(3):637-54.
2009: Arnautova Yelena A; Vila Jorge A; Martin Osvaldo A; Scheraga Harold A
What can we learn by computing 13Calpha chemical shifts for X-ray protein models?
Acta crystallographica. Section D, Biological crystallography 2009;65(Pt 7):697-703.
2009: Maisuradze Gia G; Liwo Adam; Scheraga Harold A
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
Physical review letters 2009;102(23):238102.
2009: Shen Hujun; Liwo Adam; Scheraga Harold A
An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.
The journal of physical chemistry. B 2009;113(25):8738-44.
2009: Skwierawska Agnieszka; Makowska Joanna; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.
Proteins 2009;75(4):931-53.
2009: Gahl Robert F; Pradeep Lovy; Siegel Corey R; Xu Guoqiang; Scheraga Harold A
Effects of tyrosine mutations on the conformational and oxidative folding of ribonuclease a: a comparative study.
Biochemistry 2009;48(18):3887-93.
2009: Vila Jorge A; Baldoni Héctor A; Scheraga Harold A
Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution.
Journal of computational chemistry 2009;30(6):884-92.
2009: Gahl Robert F; Scheraga Harold A
Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues.
Biochemistry 2009;48(12):2740-51.
2009: Maisuradze Gia G; Liwo Adam; Scheraga Harold A
Principal component analysis for protein folding dynamics.
Journal of molecular biology 2009;385(1):312-29.
2009: Skwierawska Agnieszka; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.
Biopolymers 2009;91(1):37-51.
2008: Skwierawska Agnieszka; Rodziewicz-Motowidlo Sylwia; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.
Biopolymers 2008;89(11):1032-44.
2008: Vila Jorge A; Aramini James M; Rossi Paolo; Kuzin Alexandre; Su Min; Seetharaman Jayaraman; Xiao Rong; Tong Liang; Montelione Gaetano T; Scheraga Harold A
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(38):14389-94.
2008: Makowski Mariusz; Sobolewski Emil; Czaplewski Cezary; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains.
The journal of physical chemistry. B 2008;112(36):11385-95.
2008: Vorobjev Yury N; Vila Jorge A; Scheraga Harold A
FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.
The journal of physical chemistry. B 2008;112(35):11122-36.
2008: Arnautova Yelena A; Scheraga Harold A
Use of decoys to optimize an all-atom force field including hydration.
Biophysical journal 2008;95(5):2434-49.
2008: Kleinerman Dana S; Czaplewski Cezary; Liwo Adam; Scheraga Harold A
Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain.
The Journal of chemical physics 2008;128(24):245103.
2008: Kang Young Kee; Scheraga Harold A
An efficient method for calculating atomic charges of peptides and proteins from electronic populations.
The journal of physical chemistry. B 2008;112(17):5470-8.
2008: Scheraga Harold A
From helix-coil transitions to protein folding.
Biopolymers 2008;89(5):479-85.
2008: Vila Jorge A; Scheraga Harold A
Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures.
Proteins 2008;71(2):641-54.
2008: Niv Masha Y; Skrabanek Lucy; Roberts Richard J; Scheraga Harold A; Weinstein Harel
Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.
Proteins 2008;71(2):631-40.
2008: Narayan Mahesh; Welker Ervin; Zhai Huili; Han Xuemei; Xu Guoqiang; McLafferty Fred W; Scheraga Harold A
Detecting native folds in mixtures of proteins that contain disulfide bonds.
Nature biotechnology 2008;26(4):427-9.
2008: Gahl Robert F; Narayan Mahesh; Xu Guoqiang; Scheraga Harold A
Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues.
Protein engineering, design & selection : PEDS 2008;21(4):223-31.
2008: Liwo Adam; Czaplewski Cezary; Oldziej Stanislaw; Scheraga Harold A
Computational techniques for efficient conformational sampling of proteins.
Current opinion in structural biology 2008;18(2):134-9.
2008: Vila Jorge A; Arnautova Yelena A; Scheraga Harold A
Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(6):1891-6.
2008: Chen Jianhan; Brooks Charles L; Scheraga Harold A
Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy.
The journal of physical chemistry. B 2008;112(2):242-9.
2008: Makowska Joanna; Baginska Katarzyna; Skwierawska Agnieszka; Liwo Adam; Chmurzynski Lech; Scheraga Harold A
Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides.
Biopolymers 2008;90(6):772-82.
2008: Makowska Joanna; Baginska Katarzyna; Liwo Adam; Chmurzynski Lech; Scheraga Harold A
Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment.
Biopolymers 2008;90(5):724-32.
2007: Murarka Rajesh K; Liwo Adam; Scheraga Harold A
Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
The Journal of chemical physics 2007;127(15):155103.
2007: Pradeep Lovy; Kurinov Igor; Ealick Steven E; Scheraga Harold A
Implementation of a k/k(0) method to identify long-range structure in transition states during conformational folding/unfolding of proteins.
Structure (London, England : 1993) 2007;15(10):1178-89.
2007: Sobolewski Emil; Makowski Mariusz; Czaplewski Cezary; Liwo Adam; Oldziej Stanislaw; Scheraga Harold A
Potential of mean force of hydrophobic association: dependence on solute size.
The journal of physical chemistry. B 2007;111(36):10765-74.
2007: Vila Jorge A; Villegas Myriam E; Baldoni Hector A; Scheraga Harold A
Predicting 13Calpha chemical shifts for validation of protein structures.
Journal of biomolecular NMR 2007;38(3):221-35.
2007: Vila Jorge A; Ripoll Daniel R; Scheraga Harold A
Use of 13Calpha chemical shifts in protein structure determination.
The journal of physical chemistry. B 2007;111(23):6577-85.
2007: Welker Ervin; Hathaway Laura; Xu Guoqiang; Narayan Mahesh; Pradeep Lovy; Shin Hang-Cheol; Scheraga Harold A
Oxidative folding and N-terminal cyclization of onconase.
Biochemistry 2007;46(18):5485-93.
2007: Jagielska Anna; Scheraga Harold A
Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent.
Journal of computational chemistry 2007;28(6):1068-82.
2007: Makowska Joanna; Rodziewicz-Motowidlo Sylwia; Baginska Katarzyna; Makowski Mariusz; Vila Jorge A; Liwo Adam; Chmurzynski Lech; Scheraga Harold A
Further evidence for the absence of polyproline II stretch in the XAO peptide.
Biophysical journal 2007;92(8):2904-17.
2007: Makowski Mariusz; Sobolewski Emil; Czaplewski Cezary; Liwo Adam; Oldziej Stanislaw; No Joo Hwan; Scheraga Harold A
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains.
The journal of physical chemistry. B 2007;111(11):2925-31.
2007: Makowski Mariusz; Liwo Adam; Maksimiak Katarzyna; Makowska Joanna; Scheraga Harold A
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems.
The journal of physical chemistry. B 2007;111(11):2917-24.
2007: Makowski Mariusz; Liwo Adam; Scheraga Harold A
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model.
The journal of physical chemistry. B 2007;111(11):2910-6.
2007: Villegas Myriam E; Vila Jorge A; Scheraga Harold A
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.
Journal of biomolecular NMR 2007;37(2):137-46.
2007: Rojas Ana V; Liwo Adam; Scheraga Harold A
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.
The journal of physical chemistry. B 2007;111(1):293-309.
2007: Liwo Adam; Khalili Mey; Czaplewski Cezary; Kalinowski Sebastian; Oldziej Stanilsaw; Wachucik Katarzyna; Scheraga Harold A
Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
The journal of physical chemistry. B 2007;111(1):260-85.
2007: Niv Masha Y; Ripoll Daniel R; Vila Jorge A; Liwo Adam; Vanamee Eva S; Aggarwal Aneel K; Weinstein Harel; Scheraga Harold A
Topology of Type II REases revisited; structural classes and the common conserved core.
Nucleic acids research 2007;35(7):2227-37.
2007: Scheraga Harold A; Khalili Mey; Liwo Adam
Protein-folding dynamics: overview of molecular simulation techniques.
Annual review of physical chemistry 2007;58():57-83.
2006: Rakowski Franciszek; Grochowski Pawel; Lesyng Bogdan; Liwo Adam; Scheraga Harold A
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.
The Journal of chemical physics 2006;125(20):204107.
2006: Pradeep Lovy; Shin Hang-Cheol; Scheraga Harold A
Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family.
FEBS letters 2006;580(21):5029-32.
2006: Dyson H Jane; Wright Peter E; Scheraga Harold A
The role of hydrophobic interactions in initiation and propagation of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):13057-61.
2006: Arnautova Yelena A; Jagielska Anna; Scheraga Harold A
A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
The journal of physical chemistry. B 2006;110(10):5025-44.
2006: Makowska Joanna; Bagiñska Katarzyna; Makowski Mariusz; Jagielska Anna; Liwo Adam; Kasprzykowski Franciszek; Chmurzyñski Lech; Scheraga Harold A
Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment.
The journal of physical chemistry. B 2006;110(9):4451-8.
2006: Makowska Joanna; Rodziewicz-Motowidlo Sylwia; Baginska Katarzyna; Vila Jorge A; Liwo Adam; Chmurzynski Lech; Scheraga Harold A
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(6):1744-9.
2006: Xu Guoqiang; Narayan Mahesh; Kurinov Igor; Ripoll Daniel R; Welker Ervin; Khalili Mey; Ealick Steven E; Scheraga Harold A
A localized specific interaction alters the unfolding pathways of structural homologues.
Journal of the American Chemical Society 2006;128(4):1204-13.
2006: Zabrouskov Vlad; Han Xuemei; Welker Ervin; Zhai Huili; Lin Cheng; van Wijk Klaas J; Scheraga Harold A; McLafferty Fred W
Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry.
Biochemistry 2006;45(3):987-92.
2006: Khalili Mey; Liwo Adam; Scheraga Harold A
Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains.
Journal of molecular biology 2006;355(3):536-47.
2005: Nanias Marian; Chinchio Maurizio; Oldziej Stanislaw; Czaplewski Cezary; Scheraga Harold A
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
Journal of computational chemistry 2005;26(14):1472-86.
2005: Day G M; Motherwell W D S; Ammon H L; Boerrigter S X M; Della Valle R G; Venuti E; Dzyabchenko A; Dunitz J D; Schweizer B; van Eijck B P; Erk P; Facelli J C; Bazterra V E; Ferraro M B; Hofmann D W M; Leusen F J J; Liang C; Pantelides C C; Karamertzanis P G; Price S L; Lewis T C; Nowell H; Torrisi A; Scheraga H A; Arnautova Y A; Schmidt M U; Verwer P
A third blind test of crystal structure prediction.
Acta crystallographica. Section B, Structural science 2005;61(Pt 5):511-27.
2005: Vila Jorge A; Ripoll Daniel R; Arnautova Yelena A; Vorobjev Yury N; Scheraga Harold A
Coupling between conformation and proton binding in proteins.
Proteins 2005;61(1):56-68.
2005: Khalili Mey; Liwo Adam; Jagielska Anna; Scheraga Harold A
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
The journal of physical chemistry. B 2005;109(28):13798-810.
2005: Khalili Mey; Liwo Adam; Rakowski Franciszek; Grochowski Pawel; Scheraga Harold A
Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.
The journal of physical chemistry. B 2005;109(28):13785-97.
2005: Xu Guoqiang; Narayan Mahesh; Scheraga Harold A
The oxidative folding rate of bovine pancreatic ribonuclease is enhanced by a covalently attached oligosaccharide.
Biochemistry 2005;44(28):9817-23.
2005: Cerovský V; Scheraga H A
Combined solid-phase/solution synthesis of large ribonuclease A C-terminal peptides containing a non-natural proline analog.
The journal of peptide research : official journal of the American Peptide Society 2005;65(6):518-28.
2005: Oldziej S; Czaplewski C; Liwo A; Chinchio M; Nanias M; Vila J A; Khalili M; Arnautova Y A; Jagielska A; Makowski M; Schafroth H D; Kazmierkiewicz R; Ripoll D R; Pillardy J; Saunders J A; Kang Y K; Gibson K D; Scheraga H A
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(21):7547-52.
2005: Ripoll Daniel R; Vila Jorge A; Scheraga Harold A
On the orientation of the backbone dipoles in native folds.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(21):7559-64.
2005: Czaplewski Cezary; Liwo Adam; Ripoll Daniel R; Scheraga Harold A
Molecular origin of anticooperativity in hydrophobic association.
The journal of physical chemistry. B 2005;109(16):8108-19.
2005: Liwo Adam; Khalili Mey; Scheraga Harold A
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2362-7.
2005: Leung H J; Xu G; Narayan M; Scheraga H A
Impact of an easily reducible disulfide bond on the oxidative folding rate of multi-disulfide-containing proteins.
The journal of peptide research : official journal of the American Peptide Society 2005;65(1):47-54.
2005: Makowska Joanna; Baginska Katarzyna; Kasprzykowski F; Vila Jorge A; Jagielska Anna; Liwo Adam; Chmurzynski Lech; Scheraga Harold A
Interplay of charge distribution and conformation in peptides: comparison of theory and experiment.
Biopolymers 2005;80(2-3):214-24.
2004: Welker Ervin; Maki Kosuke; Shastry M C Ramachandra; Juminaga Darmawi; Bhat Rajiv; Scheraga Harold A; Roder Heinrich
Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(51):17681-6.
2004: Scheraga Harold A
The thrombin-fibrinogen interaction.
Biophysical chemistry 2004;112(2-3):117-30.
2004: Gahl Robert F; Narayan Mahesh; Xu Guoqiang; Scheraga Harold A
Trimethylamine-N-oxide modulates the reductive unfolding of onconase.
Biochemical and biophysical research communications 2004;325(3):707-10.
2004: Vila Jorge A; Baldoni Héctor A; Scheraga Harold A
Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids.
Protein science : a publication of the Protein Society 2004;13(11):2939-48.
2004: Jang Seung-Hwan; Kang Dong-Ku; Chang Soo-Ik; Scheraga Harold A; Shin Hang-Cheol
High level production of bovine angiogenin in E. coli by an efficient refolding procedure.
Biotechnology letters 2004;26(19):1501-4.
2004: Dunitz Jack D; Scheraga Harold A
Exercises in prognostication: crystal structures and protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(40):14309-11.
2004: Khalili Mey; Saunders Jeffrey A; Liwo Adam; Oldziej Stanislaw; Scheraga Harold A
A united residue force-field for calcium-protein interactions.
Protein science : a publication of the Protein Society 2004;13(10):2725-35.
2004: Vila Jorge A; Baldoni Héctor A; Ripoll Daniel R; Scheraga Harold A
Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide.
Proteins 2004;57(1):87-98.
2004: Scheraga H A; Liwo A; Oldziej S; Czaplewski C; Pillardy J; Ripoll D R; Vila J A; Kazmierkiewicz R; Saunders J A; Arnautova Y A; Jagielska A; Chinchio M; Nanias M
The protein folding problem: global optimization of the force fields.
Frontiers in bioscience : a journal and virtual library 2004;9():3296-323.
2004: Fernández Ariel; Rogale Kristina; Scott Ridgway; Scheraga Harold A
Inhibitor design by wrapping packing defects in HIV-1 proteins.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(32):11640-5.
2004: Ripoll Daniel R; Vila Jorge A; Scheraga Harold A
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.
Journal of molecular biology 2004;339(4):915-25.
2004: Kamikubo Yuichi; De Guzman Roberto; Kroon Gerard; Curriden Scott; Neels Jaap G; Churchill Michael J; Dawson Philip; Oldziej Stanislaw; Jagielska Anna; Scheraga Harold A; Loskutoff David J; Dyson H Jane
Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin.
Biochemistry 2004;43(21):6519-34.
2004: Narayan Mahesh; Xu Guoqiang; Ripoll Daniel R; Zhai Huili; Breuker Kathrin; Wanjalla Celestine; Leung Howard J; Navon Amiel; Welker Ervin; McLafferty Fred W; Scheraga Harold A
Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues.
Journal of molecular biology 2004;338(4):795-809.
2004: Xu Guoqiang; Zhai Huili; Narayan Mahesh; McLafferty Fred W; Scheraga Harold A
Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry.
Chemistry & biology 2004;11(4):517-24.
2004: Dzyabchenko Alexander; Scheraga Harold A
Model for the crystal packing and conformational changes of biphenyl in incommensurate phase transitions.
Acta crystallographica. Section B, Structural science 2004;60(Pt 2):228-37.
2004: Welker Ervin; Hathaway Laura; Scheraga Harold A
A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins.
Journal of the American Chemical Society 2004;126(12):3720-1.
2004: Xu Guoqiang; Narayan Mahesh; Welker Ervin; Scheraga Harold A
Characterization of the fast-forming intermediate, des [30-75], in the reductive unfolding of onconase.
Biochemistry 2004;43(11):3246-54.
2004: Vila Jorge A; Baldoni Héctor A; Ripoll Daniel R; Ghosh Avijit; Scheraga Harold A
Polyproline II helix conformation in a proline-rich environment: a theoretical study.
Biophysical journal 2004;86(2):731-42.
2004: Czaplewski Cezary; Oldziej Stanislaw; Liwo Adam; Scheraga Harold A
Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.
Protein engineering, design & selection : PEDS 2004;17(1):29-36.
2003: Narayan Mahesh; Xu Guoqiang; Schultz Suzanne K; Scheraga Harold A
Assessing the magnitude of folding forces along the oxidative folding pathway of multi-disulfide-containing proteins.
Journal of the American Chemical Society 2003;125(52):16184-5.
2003: Vila Jorge A; Ripoll Daniel R; Scheraga Harold A
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(25):14812-6.
2003: Xu Guoqiang; Narayan Mahesh; Welker Ervin; Scheraga Harold A
A novel method to determine thermal transition curves of disulfide-containing proteins and their structured folding intermediates.
Biochemical and biophysical research communications 2003;311(2):514-7.
2003: Shin Hang-Cheol; Narayan Mahesh; Song Myeong-Cheol; Scheraga Harold A
Role of the [65-72] disulfide bond in oxidative folding of bovine pancreatic ribonuclease A.
Biochemistry 2003;42(39):11514-9.
2003: Czaplewski Cezary; Rodziewicz-Motowidlo Sylwia; Dabal Magdalena; Liwo Adam; Ripoll Daniel R; Scheraga Harold A
Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles.
Biophysical chemistry 2003;105(2-3):339-59.
2003: Narayan Mahesh; Welker Ervin; Wanjalla Celestine; Xu Guoqiang; Scheraga Harold A
Shifting the competition between the intramolecular Reshuffling reaction and the direct oxidation reaction during the oxidative folding of kinetically trapped disulfide-insecure intermediates.
Biochemistry 2003;42(36):10783-9.
2003: Narayan Mahesh; Welker Ervin; Scheraga Harold A
Characterizing the unstructured intermediates in oxidative folding.
Biochemistry 2003;42(23):6947-55.
2003: Vila Jorge A; Baldoni Héctor A; Ripoll Daniel R; Scheraga Harold A
Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts.
Journal of biomolecular NMR 2003;26(2):113-30.
2003: Bhat Rajiv; Wedemeyer William J; Scheraga Harold A
Proline isomerization in bovine pancreatic ribonuclease A. 2. Folding conditions.
Biochemistry 2003;42(19):5722-8.
2003: Saunders Jeffrey A; Scheraga Harold A
Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC.
Biopolymers 2003;68(3):318-32.
2003: Saunders Jeffrey A; Scheraga Harold A
Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search.
Biopolymers 2003;68(3):300-17.
2003: Cerovský V; Welker E; Scheraga H A
A convenient incorporation of conformationally constrained 5,5-dimethylproline into the ribonuclease A 89-124 sequence by condensation of synthetic peptide fragments.
The journal of peptide research : official journal of the American Peptide Society 2003;61(3):140-51.
2003: Narayan Mahesh; Welker Ervin; Scheraga Harold A
Native conformational tendencies in unfolded polypeptides: development of a novel method to assess native conformational tendencies in the reduced forms of multiple disulfide-bonded proteins.
Journal of the American Chemical Society 2003;125(8):2036-7.
2003: Nanias Marian; Chinchio Maurizio; Pillardy Jaroslaw; Ripoll Daniel R; Scheraga Harold A
Packing helices in proteins by global optimization of a potential energy function.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(4):1706-10.
2003: Fernández Ariel; Scheraga Harold A
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(1):113-8.
2003: Kazmierkiewicz Rajmund; Liwo Adam; Scheraga Harold A
Addition of side chains to a known backbone with defined side-chain centroids.
Biophysical chemistry 2003;100(1-3):261-80.
2002: Scheraga Harold A; Vila Jorge A; Ripoll Daniel R
Helix-coil transitions re-visited.
Biophysical chemistry 2002;101-102():255-65.
2002: Carty Robert P; Pincus Matthew R; Scheraga Harold A
Interactions that favor the native over the non-native disulfide bond among residues 58-72 in the oxidative folding of bovine pancreatic ribonuclease A.
Biochemistry 2002;41(50):14815-9.
2002: Wedemeyer William J; Welker Ervin; Scheraga Harold A
Proline cis-trans isomerization and protein folding.
Biochemistry 2002;41(50):14637-44.
2002: Navon Ami; Ittah Varda; Scheraga Harold A; Haas Elisha
Formation of the hydrophobic core of ribonuclease A through sequential coordinated conformational transitions.
Biochemistry 2002;41(48):14225-31.
2002: Vila Jorge A; Ripoll Daniel R; Baldoni Héctor A; Scheraga Harold A
Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study.
Journal of biomolecular NMR 2002;24(3):245-62.
2002: Welker Ervin; Raymond Lynne D; Scheraga Harold A; Caughey Byron
Intramolecular versus intermolecular disulfide bonds in prion proteins.
The Journal of biological chemistry 2002;277(36):33477-81.
2002: Motherwell W D Sam; Ammon Herman L; Dunitz Jack D; Dzyabchenko Alexander; Erk Peter; Gavezzotti Angelo; Hofmann Detlef W M; Leusen Frank J J; Lommerse Jos P M; Mooij Wijnand T M; Price Sarah L; Scheraga Harold; Schweizer Bernd; Schmidt Martin U; van Eijck Bouke P; Verwer Paul; Williams Donald E
Crystal structure prediction of small organic molecules: a second blind test.
Acta crystallographica. Section B, Structural science 2002;58(Pt 4):647-61.
2002: Ghosh Avijit; Elber Ron; Scheraga Harold A
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(16):10394-8.
2002: Shin Hang-Cheol; Song Myeong-Cheol; Scheraga Harold A
Effect of protein disulfide isomerase on the rate-determining steps of the folding of bovine pancreatic ribonuclease A.
FEBS letters 2002;521(1-3):77-80.
2002: English Brian P; Welker Ervin; Narayan Mahesh; Scheraga Harold A
Development of a novel method to populate native disulfide-bonded intermediates for structural characterization of proteins: implications for the mechanism of oxidative folding of RNase A.
Journal of the American Chemical Society 2002;124(18):4995-9.
2002: Kazmierkiewicz Rajmund; Liwo Adam; Scheraga Harold A
Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method.
Journal of computational chemistry 2002;23(7):715-23.
2002: Liwo Adam; Arlukowicz Piotr; Czaplewski Cezary; Oldziej Stanislaw; Pillardy Jaroslaw; Scheraga Harold A
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(4):1937-42.
2002: Wedemeyer William J; Xu Xiaobing; Welker Ervin; Scheraga Harold A
Conformational propensities of protein folding intermediates: distribution of species in the 1S, 2S, and 3S ensembles of the [C40A,C95A] mutant of bovine pancreatic ribonuclease A.
Biochemistry 2002;41(5):1483-91.
2002: Scheraga Harold A; Pillardy Jaroslaw; Liwo Adam; Lee Jooyoung; Czaplewski Cezary; Ripoll Daniel R; Wedemeyer William J; Arnautova Yelena A
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
Journal of computational chemistry 2002;23(1):28-34.
2002: Low Lawrence K; Shin Hang-Cheol; Scheraga Harold A
Oxidative folding of bovine pancreatic ribonuclease A: insight into the overall catalysis of the refolding pathway by phosphate.
Journal of protein chemistry 2002;21(1):19-27.
2002: Saunders J A; Gibson K D; Scheraga H A
Ab initio folding of multiple-chain proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():601-12.
2001: Saito K; Welker E; Scheraga H A
Folding of a disulfide-bonded protein species with free thiol(s): competition between conformational folding and disulfide reshuffling in an intermediate of bovine pancreatic ribonuclease A.
Biochemistry 2001;40(49):15002-8.
2001: Pillardy J; Arnautova Y A; Czaplewski C; Gibson K D; Scheraga H A
Conformation-family Monte Carlo: a new method for crystal structure prediction.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(22):12351-6.
2001: Welker E; Wedemeyer W J; Narayan M; Scheraga H A
Coupling of conformational folding and disulfide-bond reactions in oxidative folding of proteins.
Biochemistry 2001;40(31):9059-64.
2001: Cao A; Welker E; Scheraga H A
Effect of mutation of proline 93 on redox unfolding/folding of bovine pancreatic ribonuclease A.
Biochemistry 2001;40(29):8536-41.
2001: Welker E; Wedemeyer W J; Scheraga H A
A role for intermolecular disulfide bonds in prion diseases?
Proceedings of the National Academy of Sciences of the United States of America 2001;98(8):4334-6.
2001: Vila J A; Ripoll D R; Scheraga H A
Influence of lysine content and pH on the stability of alanine-based copolypeptides.
Biopolymers 2001;58(3):235-46.
2001: Pillardy J; Czaplewski C; Liwo A; Lee J; Ripoll D R; Kazmierkiewicz R; Oldziej S; Wedemeyer W J; Gibson K D; Arnautova Y A; Saunders J; Ye Y J; Scheraga H A
Recent improvements in prediction of protein structure by global optimization of a potential energy function.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2329-33.
2001: Welker E; Narayan M; Wedemeyer W J; Scheraga H A
Structural determinants of oxidative folding in proteins.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2312-6.
2001: Navon A; Ittah V; Landsman P; Scheraga H A; Haas E
Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein.
Biochemistry 2001;40(1):105-18.
2001: Navon A; Ittah V; Laity J H; Scheraga H A; Haas E; Gussakovsky E E
Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A.
Biochemistry 2001;40(1):93-104.
2001: Scheraga H A; Wedemeyer W J; Welker E
Bovine pancreatic ribonuclease A: oxidative and conformational folding studies.
Methods in enzymology 2001;341():189-221.
2000: Narayan M; Welker E; Wedemeyer W J; Scheraga H A
Oxidative folding of proteins.
Accounts of chemical research 2000;33(11):805-12.
2000: Vila J A; Ripoll D R; Scheraga H A
Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(24):13075-9.
2000: Shin H C; Scheraga H A
Catalysis of the oxidative folding of bovine pancreatic ribonuclease A by protein disulfide isomerase.
Journal of molecular biology 2000;300(4):995-1003.
2000: Czaplewski C; Rodziewicz-Motowidlo S; Liwo A; Ripoll D R; Wawak R J; Scheraga H A
Molecular simulation study of cooperativity in hydrophobic association.
Protein science : a publication of the Protein Society 2000;9(6):1235-45.
2000: Low L K; Shin H C; Narayan M; Wedemeyer W J; Scheraga H A
Acceleration of oxidative folding of bovine pancreatic ribonuclease A by anion-induced stabilization and formation of structured native-like intermediates.
FEBS letters 2000;472(1):67-72.
2000: Song M C; Scheraga H A
Formation of native structure by intermolecular thiol-disulfide exchange reactions without oxidants in the folding of bovine pancreatic ribonuclease A.
FEBS letters 2000;471(2-3):177-81.
2000: Wedemeyer W J; Welker E; Narayan M; Scheraga H A
Disulfide bonds and protein folding.
Biochemistry 2000;39(15):4207-16.
2000: Xiong Y; Juminaga D; Swapna G V; Wedemeyer W J; Scheraga H A; Montelione G T
Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A.
Protein science : a publication of the Protein Society 2000;9(2):421-6.
1999: Laity J H; Montelione G T; Scheraga H A
Comparison of local and global stability of an analogue of a disulfide-folding intermediate with those of the wild-type protein in bovine pancreatic ribonuclease A: identification of specific regions of stable structure along the oxidative folding pathway.
Biochemistry 1999;38(50):16432-42.
1999: Welker E; Narayan M; Volles M J; Scheraga H A
Two new structured intermediates in the oxidative folding of RNase A.
FEBS letters 1999;460(3):477-9.
1999: Ripoll D R; Vila J A; Villegas M E; Scheraga H A
On the pH-conformational dependence of the unblocked SYPYD peptide.
Journal of molecular biology 1999;292(2):431-40.
1999: Shin H C; Scheraga H A
Effect of protein disulfide isomerase on the regeneration of bovine ribonuclease A with dithiothreitol.
FEBS letters 1999;456(1):143-5.
1999: Volles M J; Xu X; Scheraga H A
Distribution of disulfide bonds in the two-disulfide intermediates in the regeneration of bovine pancreatic ribonuclease A: further insights into the folding process.
Biochemistry 1999;38(22):7284-93.
1999: Liwo A; Lee J; Ripoll D R; Pillardy J; Scheraga H A
Protein structure prediction by global optimization of a potential energy function.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(10):5482-5.
1999: Iwaoka M; Wedemeyer W J; Scheraga H A
Conformational unfolding studies of three-disulfide mutants of bovine pancreatic ribonuclease A and the coupling of proline isomerization to disulfide redox reactions.
Biochemistry 1999;38(9):2805-15.
1999: Lee J; Liwo A; Scheraga H A
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(5):2025-30.
1999: Maurer M C; Trosset J Y; Lester C C; DiBella E E; Scheraga H A
New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program.
Proteins 1999;34(1):29-48.
1999: Welker E; Scheraga H A
Use of benzyl mercaptan for direct preparation of long polypeptide benzylthio esters as substrates of subtiligase.
Biochemical and biophysical research communications 1999;254(1):147-51.
1999: Lee J; Liwo A; Ripoll D R; Pillardy J; Scheraga H A
Calculation of protein conformation by global optimization of a potential energy function.
Proteins 1999;Suppl 3():204-8.
1998: Vila J A; Ripoll D R; Villegas M E; Vorobjev Y N; Scheraga H A
Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices.
Biophysical journal 1998;75(6):2637-46.
1998: Scheraga H A
Theory of hydrophobic interactions.
Journal of biomolecular structure & dynamics 1998;16(2):447-60.
1998: Juminaga D; Wedemeyer W J; Scheraga H A
Proline isomerization in bovine pancreatic ribonuclease A. 1. Unfolding conditions.
Biochemistry 1998;37(33):11614-20.
1998: Ripoll D R; Liwo A; Scheraga H A
New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin.
Biopolymers 1998;46(2):117-26.
1998: Trosset J Y; Scheraga H A
Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(14):8011-5.
1998: Xu X; Scheraga H A
Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40-95] disulfide bond.
Biochemistry 1998;37(20):7561-71.
1998: DiBella E E; Scheraga H A
Thrombin specificity: further evidence for the importance of the beta-insertion loop and Trp96. Implications of the hydrophobic interaction between Trp96 and Pro60B Pro60C for the activity of thrombin.
Journal of protein chemistry 1998;17(3):197-208.
1998: Maurer M C; Peng J L; An S S; Trosset J Y; Henschen-Edman A; Scheraga H A
Structural examination of the influence of phosphorylation on the binding of fibrinopeptide A to bovine thrombin.
Biochemistry 1998;37(17):5888-902.
1998: Hao M H; Scheraga H A
Molecular mechanisms for cooperative folding of proteins.
Journal of molecular biology 1998;277(4):973-83.
1998: Houry W A; Sauder J M; Roder H; Scheraga H A
Definition of amide protection factors for early kinetic intermediates in protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(8):4299-302.
1998: Iwaoka M; Juminaga D; Scheraga H A
Regeneration of three-disulfide mutants of bovine pancreatic ribonuclease A missing the 65-72 disulfide bond: characterization of a minor folding pathway of ribonuclease A and kinetic roles of Cys65 and Cys72.
Biochemistry 1998;37(13):4490-501.
1998: Rothwarf D M; Li Y J; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A: detailed kinetic analysis of two independent folding pathways.
Biochemistry 1998;37(11):3767-76.
1998: Rothwarf D M; Li Y J; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A: identification of two nativelike three-disulfide intermediates involved in separate pathways.
Biochemistry 1998;37(11):3760-6.
1998: Thannhauser T W; Sherwood R W; Scheraga H A
Determination of the cysteine and cystine content of proteins by amino acid analysis: application to the characterization of disulfide-coupled folding intermediates.
Journal of protein chemistry 1998;17(1):37-43.
1997: Lester C C; Xu X; Laity J H; Shimotakahara S; Scheraga H A
Regeneration studies of an analog of ribonuclease A missing disulfide bonds 65-72 and 40-95.
Biochemistry 1997;36(42):13068-76.
1997: Laity J H; Lester C C; Shimotakahara S; Zimmerman D E; Montelione G T; Scheraga H A
Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A.
Biochemistry 1997;36(42):12683-99.
1997: Juminaga D; Wedemeyer W J; Garduño-Júarez R; McDonald M A; Scheraga H A
Tyrosyl interactions in the folding and unfolding of bovine pancreatic ribonuclease A: a study of tyrosine-to-phenylalanine mutants.
Biochemistry 1997;36(33):10131-45.
1997: Shimotakahara S; Rios C B; Laity J H; Zimmerman D E; Scheraga H A; Montelione G T
NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms.
Biochemistry 1997;36(23):6915-29.
1997: Wedemeyer W J; Ashton R W; Scheraga H A
Kinetics of competitive binding with application to thrombin complexes.
Analytical biochemistry 1997;248(1):130-40.
1997: Thannhauser T W; Rothwarf D M; Scheraga H A
Kinetic studies of the regeneration of recombinant hirudin variant 1 with oxidized and reduced dithiothreitol.
Biochemistry 1997;36(8):2154-65.
1996: Ripoll D R; Vorobjev Y N; Liwo A; Vila J A; Scheraga H A
Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.
Journal of molecular biology 1996;264(4):770-83.
1996: Rothwarf D M; Scheraga H A
Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme.
Biochemistry 1996;35(43):13797-807.
1996: Sendak R A; Rothwarf D M; Wedemeyer W J; Houry W A; Scheraga H A
Kinetic and thermodynamic studies of the folding/unfolding of a tryptophan-containing mutant of ribonuclease A.
Biochemistry 1996;35(39):12978-92.
1996: Rabow A A; Scheraga H A
Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator.
Protein science : a publication of the Protein Society 1996;5(9):1800-15.
1996: Houry W A; Scheraga H A
Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange.
Biochemistry 1996;35(36):11734-46.
1996: Houry W A; Scheraga H A
Nature of the unfolded state of ribonuclease A: effect of cis-trans X-Pro peptide bond isomerization.
Biochemistry 1996;35(36):11719-33.
1996: Houry W A; Rothwarf D M; Scheraga H A
Circular dichroism evidence for the presence of burst-phase intermediates on the conformational folding pathway of ribonuclease A.
Biochemistry 1996;35(31):10125-33.
1996: Hao M H; Scheraga H A
How optimization of potential functions affects protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(10):4984-9.
1996: Xu X; Rothwarf D M; Scheraga H A
Nonrandom distribution of the one-disulfide intermediates in the regeneration of ribonuclease A.
Biochemistry 1996;35(20):6406-17.
1996: DiBella E E; Scheraga H A
The role of the insertion loop around tryptophan 148 in tthe activity of thrombin.
Biochemistry 1996;35(14):4427-33.
1996: Wawak R J; Gibson K D; Liwo A; Scheraga H A
Theoretical prediction of a crystal structure.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(5):1743-6.
1996: Kombo D C; Némethy G; Gibson K D; Rackovsky S; Scheraga H A
Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor.
Journal of molecular biology 1996;256(3):517-32.
1996: Dodge R W; Scheraga H A
Folding and unfolding kinetics of the proline-to-alanine mutants of bovine pancreatic ribonuclease A.
Biochemistry 1996;35(5):1548-59.
1996: Kombo D C; Némethy G; Gibson K D; Ross J B; Rackovsky S; Scheraga H A
Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor.
Journal of protein chemistry 1996;15(1):77-86.
1995: Buckler D R; Haas E; Scheraga H A
Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved noradiative dynamic excitation energy transfer between site-specific extrinsic probes.
Biochemistry 1995;34(49):15965-78.
1995: Lester C C; Wang B; Wu R; Scheraga H A
Structure-function studies of mEGF: probing the type I beta-turn between residues 25 and 26.
Journal of protein chemistry 1995;14(8):753-62.
1995: Paterlini M G; Némethy G; Scheraga H A
The energy of formation of internal loops in triple-helical collagen polypeptides.
Biopolymers 1995;35(6):607-19.
1995: Houry W A; Rothwarf D M; Scheraga H A
The nature of the initial step in the conformational folding of disulphide-intact ribonuclease A.
Nature structural biology 1995;2(6):495-503.
1995: Li Y J; Rothwarf D M; Scheraga H A
Mechanism of reductive protein unfolding.
Nature structural biology 1995;2(6):489-94.
1995: Ashton R W; Scheraga H A
Preparation and characterization of anhydrothrombin.
Biochemistry 1995;34(19):6454-63.
1995: Vitagliano L; Némethy G; Zagari A; Scheraga H A
Structure of the type I collagen molecule based on conformational energy computations: the triple-stranded helix and the N-terminal telopeptide.
Journal of molecular biology 1995;247(1):69-80.
1995: Augspurger J D; Bindra V A; Scheraga H A; Kuki A
Helical stability of de novo designed alpha-aminoisobutyric acid-rich peptides at high temperatures.
Biochemistry 1995;34(8):2566-76.
1995: DiBella E E; Maurer M C; Scheraga H A
Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin.
The Journal of biological chemistry 1995;270(1):163-9.
1994: Denton M E; Rothwarf D M; Scheraga H A
Kinetics of folding of guanidine-denatured hen egg white lysozyme and carboxymethyl(Cys6,Cys127)-lysozyme: a stopped-flow absorbance and fluorescence study.
Biochemistry 1994;33(37):11225-36.
1994: Talluri S; Rothwarf D M; Scheraga H A
Structural characterization of a three-disulfide intermediate of ribonuclease A involved in both the folding and unfolding pathways.
Biochemistry 1994;33(34):10437-49.
1994: Dodge R W; Laity J H; Rothwarf D M; Shimotakahara S; Scheraga H A
Folding pathway of guanidine-denatured disulfide-intact wild-type and mutant bovine pancreatic ribonuclease A.
Journal of protein chemistry 1994;13(4):409-21.
1994: Liwo A; Oldziej S; Ciarkowski J; Kupryszewski G; Pincus M R; Wawak R J; Rackovsky S; Scheraga H A
Prediction of conformation of rat galanin in the presence and absence of water with the use of Monte Carlo methods and the ECEPP/3 force field.
Journal of protein chemistry 1994;13(4):375-80.
1994: Nayeem A; Scheraga H A
A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions.
Journal of protein chemistry 1994;13(3):283-96.
1994: Houry W A; Rothwarf D M; Scheraga H A
A very fast phase in the refolding of disulfide-intact ribonuclease A: implications for the refolding and unfolding pathways.
Biochemistry 1994;33(9):2516-30.
1994: Liwo A; Gibson K D; Scheraga H A; Brandt-Rauf P W; Monaco R; Pincus M R
Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP.
Journal of protein chemistry 1994;13(2):237-51.
1994: Zagari A; Palmer K A; Gibson K D; Némethy G; Scheraga H A
The effect of the l-azetidine-2-carboxylic acid residue on protein conformation. IV. Local substitutions in the collagen triple helix.
Biopolymers 1994;34(1):51-60.
1993: Liwo A; Pincus M R; Wawak R J; Rackovsky S; Scheraga H A
Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide.
Protein science : a publication of the Protein Society 1993;2(10):1715-31.
1993: Liwo A; Pincus M R; Wawak R J; Rackovsky S; Scheraga H A
Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment.
Protein science : a publication of the Protein Society 1993;2(10):1697-714.
1993: Hao M H; Pincus M R; Rackovsky S; Scheraga H A
Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations.
Biochemistry 1993;32(37):9614-31.
1993: Rabow A A; Scheraga H A
Lattice neural network minimization. Application of neural network optimization for locating the global-minimum conformations of proteins.
Journal of molecular biology 1993;232(4):1157-68.
1993: Vitagliano L; Némethy G; Zagari A; Scheraga H A
Stabilization of the triple-helical structure of natural collagen by side-chain interactions.
Biochemistry 1993;32(29):7354-9.
1993: Moy F J; Li Y C; Rauenbuehler P; Winkler M E; Scheraga H A; Montelione G T
Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints.
Biochemistry 1993;32(29):7334-53.
1993: Rothwarf D M; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A. 4. Temperature dependence of the regeneration rate.
Biochemistry 1993;32(10):2698-703.
1993: Rothwarf D M; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A. 3. Dependence on the nature of the redox reagent.
Biochemistry 1993;32(10):2690-7.
1993: Rothwarf D M; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A. 2. Kinetics of regeneration.
Biochemistry 1993;32(10):2680-9.
1993: Rothwarf D M; Scheraga H A
Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution.
Biochemistry 1993;32(10):2671-9.
1993: Buckler D R; Haas E; Scheraga H A
C-terminal labeling of ribonuclease A with an extrinsic fluorescent probe by carboxypeptidase Y-catalyzed transpeptidation in the presence of urea.
Analytical biochemistry 1993;209(1):20-31.
1993: Laity J H; Shimotakahara S; Scheraga H A
Expression of wild-type and mutant bovine pancreatic ribonuclease A in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(2):615-9.
1992: Rothwarf D M; Scheraga H A
Equilibrium and kinetic constants for the thiol-disulfide interchange reaction between glutathione and dithiothreitol.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(17):7944-8.
1992: Williams R L; Vila J; Perrot G; Scheraga H A
Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor.
Proteins 1992;14(1):110-9.
1992: Vila J; Williams R L; Grant J A; Wójcik J; Scheraga H A
The intrinsic helix-forming tendency of L-alanine.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(16):7821-5.
1992: Hao M H; Rackovsky S; Liwo A; Pincus M R; Scheraga H A
Effects of compact volume and chain stiffness on the conformations of native proteins.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(14):6614-8.
1992: Zheng Z; Ashton R W; Ni F; Scheraga H A
Thrombin hydrolysis of an N-terminal peptide from fibrinogen Lille: kinetic and NMR studies.
Biochemistry 1992;31(18):4426-31.
1992: Scheraga H A
Contribution of physical chemistry to an understanding of protein structure and function.
Protein science : a publication of the Protein Society 1992;1(5):691-3.
1992: Montelione G T; Wüthrich K; Burgess A W; Nice E C; Wagner G; Gibson K D; Scheraga H A
Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints.
Biochemistry 1992;31(1):236-49.
1991: Fossey S A; Némethy G; Gibson K D; Scheraga H A
Conformational energy studies of beta-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains.
Biopolymers 1991;31(13):1529-41.
1991: Shapiro A B; Gibson K D; Scheraga H A; McCarty R E
Fluorescence resonance energy transfer mapping of the fourth of six nucleotide-binding sites of chloroplast coupling factor 1.
The Journal of biological chemistry 1991;266(26):17276-85.
1991: Beals J M; Haas E; Krausz S; Scheraga H A
Conformational studies of a peptide corresponding to a region of the C-terminus of ribonuclease A: implications as a potential chain-folding initiation site.
Biochemistry 1991;30(31):7680-92.
1991: Glasser L; Scheraga H A
Investigation of a physical basis for conformational similarity in proteins.
Journal of protein chemistry 1991;10(3):273-85.
1991: Simon I; Glasser L; Scheraga H A
Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(9):3661-5.
1991: Denton M E; Scheraga H A
Spectroscopic, immunochemical, and thermodynamic properties of carboxymethyl(Cys6, Cys127)-hen egg white lysozyme.
Journal of protein chemistry 1991;10(2):213-32.
1991: Ripoll D R; Vásquez M J; Scheraga H A
The electrostatically driven Monte Carlo method: application to conformational analysis of decaglycine.
Biopolymers 1991;31(3):319-30.
1991: Witmer M R; Falcomer C M; Weiner M P; Kay M S; Begley T P; Ganem B; Scheraga H A
U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems.
Nucleic acids research 1991;19(1):1-4.
1991: Vila J; Williams R L; Vásquez M; Scheraga H A
Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor.
Proteins 1991;10(3):199-218.
1991: Ripoll D R; Piela L; Vásquez M; Scheraga H A
On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor.
Proteins 1991;10(3):188-98.
1990: Walker F; Nice E; Fabri L; Moy F J; Liu J F; Wu R; Scheraga H A; Burgess A W
Resistance to receptor-mediated degradation of a murine epidermal growth factor analogue (EGF-Val-47) potentiates its mitogenic activity.
Biochemistry 1990;29(47):10635-40.
1990: Talluri S; Scheraga H A
Amide H/D exchange in the thermal transition of bovine pancreatic ribonuclease A.
Biochemical and biophysical research communications 1990;172(2):800-3.
1990: Adler M; Scheraga H A
Identification of a new site of conformational heterogeneity in unfolded ribonuclease A.
Journal of protein chemistry 1990;9(5):583-8.
1990: Chen J M; Lee G; Brandt-Rauf P W; Murphy R B; Gibson K D; Scheraga H A; Rackovsky S; Pincus M R
Conformations of the central transforming region (Ile 55-Met 67) of the p21 protein and their relationship to activation of the protein.
International journal of peptide and protein research 1990;36(3):247-54.
1990: Adler M; Scheraga H A
Nonnative isomers of proline-93 and -114 predominate in heat-unfolded ribonuclease A.
Biochemistry 1990;29(36):8211-6.
1990: Ripoll D R; Scheraga H A
On the multiple-minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven Monte Carlo method to the 20-residue membrane-bound portion of melittin.
Biopolymers 1990;30(1-2):165-76.
1990: Altmann K H; Wójcik J; Vásquez M; Scheraga H A
Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly (hydroxybutylglutamine-co-L-proline).
Biopolymers 1990;30(1-2):107-20.
1990: Zagari A; Némethy G; Scheraga H A
The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. III. Collagen-like poly(tripeptide)s.
Biopolymers 1990;30(9-10):967-74.
1990: Zagari A; Némethy G; Scheraga H A
The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. II. Homopolymers and copolymers.
Biopolymers 1990;30(9-10):961-6.
1990: Zagari A; Némethy G; Scheraga H A
The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. I. Conformations of the residue and of dipeptides.
Biopolymers 1990;30(9-10):951-9.
1990: Grant J A; Williams R L; Scheraga H A
Ab initio self-consistent field and potential-dependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N'-methyl-alanineamide.
Biopolymers 1990;30(9-10):929-49.
1989: Moy F J; Scheraga H A; Liu J F; Wu R; Montelione G T
Conformational characterization of a single-site mutant of murine epidermal growth factor (EGF) by 1H NMR provides evidence that leucine-47 is involved in the interactions with the EGF receptor.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(24):9836-40.
1989: Roterman I K; Lambert M H; Gibson K D; Scheraga H A
A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.
Journal of biomolecular structure & dynamics 1989;7(3):421-53.
1989: Roterman I K; Gibson K D; Scheraga H A
A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9.
Journal of biomolecular structure & dynamics 1989;7(3):391-419.
1989: Weiner M P; Scheraga H A
A method for the cloning of unpurified single-stranded oligonucleotides.
Nucleic acids research 1989;17(17):7113.
1989: Weiner M P; Scheraga H A
A set of Macintosh computer programs for the design and analysis of synthetic genes.
Computer applications in the biosciences : CABIOS 1989;5(3):191-8.
1989: Ni F; Konishi Y; Bullock L D; Rivetna M N; Scheraga H A
High-resolution NMR studies of fibrinogen-like peptides in solution: structural basis for the bleeding disorder caused by a single mutation of Gly(12) to Val(12) in the A alpha chain of human fibrinogen Rouen.
Biochemistry 1989;28(7):3106-19.
1989: Ni F; Meinwald Y C; Vásquez M; Scheraga H A
High-resolution NMR studies of fibrinogen-like peptides in solution: structure of a thrombin-bound peptide corresponding to residues 7-16 of the A alpha chain of human fibrinogen.
Biochemistry 1989;28(7):3094-105.
1989: Ni F; Konishi Y; Frazier R B; Scheraga H A; Lord S T
High-resolution NMR studies of fibrinogen-like peptides in solution: interaction of thrombin with residues 1-23 of the A alpha chain of human fibrinogen.
Biochemistry 1989;28(7):3082-94.
1989: Ripoll D R; Scheraga H A
The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin.
Journal of protein chemistry 1989;8(2):263-87.
1988: Ray P; Moy F J; Montelione G T; Liu J F; Narang S A; Scheraga H A; Wu R
Structure-function studies of murine epidermal growth factor: expression and site-directed mutagenesis of epidermal growth factor gene.
Biochemistry 1988;27(19):7289-95.
1988: Weiner M P; Thannhauser T W; Laity J H; Benning M E; Lee D P; Scheraga H A
Plasmid purification using reverse-phase high performance liquid chromatography resin PRP-infinity.
Nucleic acids research 1988;16(16):8185.
1988: Kikuchi T; Némethy G; Scheraga H A
Prediction of probable pathways of folding in globular proteins.
Journal of protein chemistry 1988;7(4):491-507.
1988: Kikuchi T; Némethy G; Scheraga H A
Prediction of the packing arrangement of strands in beta-sheets of globular proteins.
Journal of protein chemistry 1988;7(4):473-90.
1988: Kikuchi T; Némethy G; Scheraga H A
Prediction of the location of structural domains in globular proteins.
Journal of protein chemistry 1988;7(4):427-71.
1988: Milburn P J; Scheraga H A
Local interactions favor the native 8-residue disulfide loop in the oxidation of a fragment corresponding to the sequence Ser-50-Met-79 derived from bovine pancreatic ribonuclease A.
Journal of protein chemistry 1988;7(4):377-98.
1988: Ni F; Scheraga H A; Lord S T
High-resolution NMR studies of fibrinogen-like peptides in solution: resonance assignments and conformational analysis of residues 1-23 of the A alpha chain of human fibrinogen.
Biochemistry 1988;27(12):4481-91.
1988: Adler M; Scheraga H A
Structural studies of a folding intermediate of bovine pancreatic ribonuclease A by continuous recycled flow.
Biochemistry 1988;27(7):2471-80.
1988: Vali Z; Scheraga H A
Localization of the binding site on fibrin for the secondary binding site of thrombin.
Biochemistry 1988;27(6):1956-63.
1988: Milburn P J; Meinwald Y C; Takahashi S; Ooi T; Scheraga H A
Chain reversals in model peptides: studies of cystine-containing cyclic peptides. II. Effects of valyl residues and possible i-to-(i + 3) attractive ionic interactions on cyclization of [Cys1], [Cys6] hexapeptides.
International journal of peptide and protein research 1988;31(3):311-21.
1988: Montelione G T; Wüthrich K; Scheraga H A
Sequence-specific 1H NMR assignments and identification of slowly exchanging amide protons in murine epidermal growth factor.
Biochemistry 1988;27(6):2235-43.
1988: Glasser L; Scheraga H A
Calculations on crystal packing of a flexible molecule, Leu-enkephalin.
Journal of molecular biology 1988;199(3):513-24.
1988: Vásquez M; Scheraga H A
Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data.
Journal of biomolecular structure & dynamics 1988;5(4):757-84.
1988: Vásquez M; Scheraga H A
Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data.
Journal of biomolecular structure & dynamics 1988;5(4):705-55.
1988: Pincus M R; Murphy R B; Carty R P; Chen J; Shah D; Scheraga H A
Conformational analysis of possible biologically active (receptor-bound) conformations of peptides derived from cholecystokinin, cerulein and little gastrin and the opiate peptide, Met-enkephalin.
Peptides 1988;9 Suppl 1():145-52.
1987: Pincus M R; Brandt-Rauf P W; Carty R P; Lubowsky J; Avitable M; Gibson K D; Scheraga H A
Conformational effects of substituting amino acids for glutamine-61 on the central transforming region of the P21 proteins.
Proceedings of the National Academy of Sciences of the United States of America 1987;84(23):8375-9.
1987: Li Z; Scheraga H A
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1987;84(19):6611-5.
1987: Swadesh J K; Mui P W; Scheraga H A
Thermodynamics of the quenching of tyrosyl fluorescence by dithiothreitol.
Biochemistry 1987;26(18):5761-9.
1987: Purisima E O; Scheraga H A
An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin.
Journal of molecular biology 1987;196(3):697-709.
1987: Pincus M R; Carty R P; Chen J; Lubowsky J; Avitable M; Shah D; Scheraga H A; Murphy R B
On the biologically active structures of cholecystokinin, little gastrin, and enkephalin in the gastrointestinal system.
Proceedings of the National Academy of Sciences of the United States of America 1987;84(14):4821-5.
1980: Isogai Y; Némethy G; Rackovsky S; Leach S J; Scheraga H A
Characterization of multiple bends in proteins.
Biopolymers 1980;19(6):1183-210.

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