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Jeffrey Skolnick

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.

Research Profile (preview)

Concepts & Ideas

Physiology

Protein Folding

Chemicals & Drugs

Activities & Behaviors

Genes & Molecular Sequences

Amino Acid Sequence

Occupations

Procedures

Sequence Alignment

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Co-Publications
Name
52
Kolinski, Andrzej
19
Zhang, Yang
14
Godzik, Adam
13
Arakaki, Adrian
9
Kihara, Daisuke
9
Ortiz, AR
6
Brooks, Charles
6
Brylinski, Michal
6
Rotkiewicz, Piotr
6
Reva, BA
5
Fetrow, Jacquelyn
5
Finkelstein, Alexei
5
Lu, Hui
4
Pandit, Shashi
4
Hu, WP

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Publications

TOP 3
Gao Mu; Skolnick Jeffrey
A threading-based method for the prediction of DNA-binding proteins with application to the human genome.
Skolnick Jeffrey; Arakaki Adrian K; Lee Seung Yup; Brylinski Michal
The continuity of protein structure space is an intrinsic property of proteins.
Skolnick Jeffrey; Brylinski Michal
FINDSITE: a combined evolution/structure-based approach to protein function prediction.

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All Publications

2009: Gao Mu; Skolnick Jeffrey
A threading-based method for the prediction of DNA-binding proteins with application to the human genome.
PLoS computational biology 2009;5(11):e1000567.
2009: Skolnick Jeffrey; Arakaki Adrian K; Lee Seung Yup; Brylinski Michal
The continuity of protein structure space is an intrinsic property of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(37):15690-5.
2009: Skolnick Jeffrey; Brylinski Michal
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
Briefings in bioinformatics 2009;10(4):378-91.
2009: Brylinski Michal; Skolnick Jeffrey
FINDSITE: a threading-based approach to ligand homology modeling.
PLoS computational biology 2009;5(6):e1000405.
2009: Skolnick Jeffrey; Friesner Richard A
Editorial overview.
Current opinion in structural biology 2009;19(2):117-9.
2009: Gao Mu; Skolnick Jeffrey
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.
PLoS computational biology 2009;5(3):e1000341.
2009: Zhou Hongyi; Skolnick Jeffrey
Protein structure prediction by pro-Sp3-TASSER.
Biophysical journal 2009;96(6):2119-27.
2009: Zhou Hongyi; Pandit Shashi B; Skolnick Jeffrey
Performance of the Pro-sp3-TASSER server in CASP8.
Proteins 2009;77 Suppl 9():123-7.
2009: Arakaki Adrian K; Huang Ying; Skolnick Jeffrey
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.
BMC bioinformatics 2009;10():107.
2008: Arakaki Adrian K; Skolnick Jeffrey; McDonald John F
Marker metabolites can be therapeutic targets as well.
Nature 2008;456(7221):443.
2008: Lee Seung Yup; Skolnick Jeffrey
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints.
Biophysical journal 2008;95(4):1956-64.
2008: Gao Mu; Skolnick Jeffrey
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
Nucleic acids research 2008;36(12):3978-92.
2008: Brylinski Michal; Skolnick Jeffrey
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints.
Journal of computational chemistry 2008;29(10):1574-88.
2008: Somarelli J A; Lee S Y; Skolnick J; Herrera R J
Structure-based classification of 45 FK506-binding proteins.
Proteins 2008;72(1):197-208.
2008: Rotkiewicz Piotr; Skolnick Jeffrey
Fast procedure for reconstruction of full-atom protein models from reduced representations.
Journal of computational chemistry 2008;29(9):1460-5.
2008: Jagielska Anna; Wroblewska Liliana; Skolnick Jeffrey
Protein model refinement using an optimized physics-based all-atom force field.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(24):8268-73.
2008: Kim Ryangguk; Skolnick Jeffrey
Assessment of programs for ligand binding affinity prediction.
Journal of computational chemistry 2008;29(8):1316-31.
2008: Zhou Hongyi; Skolnick Jeffrey
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential.
Proteins 2008;71(3):1211-8.
2008: Wroblewska Liliana; Jagielska Anna; Skolnick Jeffrey
Development of a physics-based force field for the scoring and refinement of protein models.
Biophysical journal 2008;94(8):3227-40.
2008: Chen Huiling; Skolnick Jeffrey
M-TASSER: an algorithm for protein quaternary structure prediction.
Biophysical journal 2008;94(3):918-28.
2008: Brylinski Michal; Skolnick Jeffrey
What is the relationship between the global structures of apo and holo proteins?
Proteins 2008;70(2):363-77.
2008: Brylinski Michal; Skolnick Jeffrey
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(1):129-34.
2008: Pandit Shashi Bhushan; Skolnick Jeffrey
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.
BMC bioinformatics 2008;9():531.
2008: Arakaki Adrian K; Mezencev Roman; Bowen Nathan J; Huang Ying; McDonald John F; Skolnick Jeffrey
Identification of metabolites with anticancer properties by computational metabolomics.
Molecular cancer 2008;7():57.
2008: Thomas Sara H; Wagner Ryan D; Arakaki Adrian K; Skolnick Jeffrey; Kirby John R; Shimkets Lawrence J; Sanford Robert A; Löffler Frank E
The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria.
PloS one 2008;3(5):e2103.
2007: Martinez Robert J; Beazley Melanie J; Taillefert Martial; Arakaki Adrian K; Skolnick Jeffrey; Sobecky Patricia A
Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils.
Environmental microbiology 2007;9(12):3122-33.
2007: Zhou Hongyi; Skolnick Jeffrey
Ab initio protein structure prediction using chunk-TASSER.
Biophysical journal 2007;93(5):1510-8.
2007: Wroblewska Liliana; Skolnick Jeffrey
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking.
Journal of computational chemistry 2007;28(12):2059-66.
2007: Lee Seung Yup; Skolnick Jeffrey
Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions.
Proteins 2007;68(1):39-47.
2007: Borreguero Jose M; Skolnick Jeffrey
Benchmarking of TASSER in the ab initio limit.
Proteins 2007;68(1):48-56.
2007: Jagielska Anna; Skolnick Jeffrey
Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field.
Journal of computational chemistry 2007;28(10):1648-57.
2007: Ding Zhaofeng; Wang Huachun; Liang Xiangyang; Morris Erin R; Gallazzi Fabio; Pandit Shashi; Skolnick Jeffrey; Walker John C; Van Doren Steven R
Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase.
Biochemistry 2007;46(10):2684-96.
2007: Yang Jae Shick; Chen William W; Skolnick Jeffrey; Shakhnovich Eugene I
All-atom ab initio folding of a diverse set of proteins.
Structure (London, England : 1993) 2007;15(1):53-63.
2007: Zhou Hongyi; Pandit Shashi B; Lee Seung Yup; Borreguero Jose; Chen Huiling; Wroblewska Liliana; Skolnick Jeffrey
Analysis of TASSER-based CASP7 protein structure prediction results.
Proteins 2007;69 Suppl 8():90-7.
2007: Wu Sitao; Skolnick Jeffrey; Zhang Yang
Ab initio modeling of small proteins by iterative TASSER simulations.
BMC biology 2007;5():17.
2006: Pandit Shashi Bhushan; Zhang Yang; Skolnick Jeffrey
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal 2006;91(11):4180-90.
2006: Szilágyi András; Skolnick Jeffrey
Efficient prediction of nucleic acid binding function from low-resolution protein structures.
Journal of molecular biology 2006;358(3):922-33.
2006: Grimm Vera; Zhang Yang; Skolnick Jeffrey
Benchmarking of dimeric threading and structure refinement.
Proteins 2006;63(3):457-65.
2006: Lee Seung Yup; Zhang Yang; Skolnick Jeffrey
TASSER-based refinement of NMR structures.
Proteins 2006;63(3):451-6.
2006: Skolnick Jeffrey
In quest of an empirical potential for protein structure prediction.
Current opinion in structural biology 2006;16(2):166-71.
2006: Zhang Yang; Devries Mark E; Skolnick Jeffrey
Structure modeling of all identified G protein-coupled receptors in the human genome.
PLoS computational biology 2006;2(2):e13.
2006: Zhang Yang; Hubner Isaac A; Arakaki Adrian K; Shakhnovich Eugene; Skolnick Jeffrey
On the origin and highly likely completeness of single-domain protein structures.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(8):2605-10.
2006: Arakaki Adrian K; Tian Weidong; Skolnick Jeffrey
High precision multi-genome scale reannotation of enzyme function by EFICAz.
BMC genomics 2006;7():315.
2005: Szilágyi András; Grimm Vera; Arakaki Adrián K; Skolnick Jeffrey
Prediction of physical protein-protein interactions.
Physical biology 2005;2(2):S1-16.
2005: Bindewald Eckart; Skolnick Jeffrey
A scoring function for docking ligands to low-resolution protein structures.
Journal of computational chemistry 2005;26(4):374-83.
2005: Skolnick Jeffrey
Putting the pathway back into protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2265-6.
2005: Zhang Yang; Skolnick Jeffrey
The protein structure prediction problem could be solved using the current PDB library.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(4):1029-34.
2005: Zhang Yang; Arakaki Adrian K; Skolnick Jeffrey
TASSER: an automated method for the prediction of protein tertiary structures in CASP6.
Proteins 2005;61 Suppl 7():91-8.
2005: Zhang Yang; Skolnick Jeffrey
TM-align: a protein structure alignment algorithm based on the TM-score.
Nucleic acids research 2005;33(7):2302-9.
2004: Zhang Yang; Skolnick Jeffrey
Scoring function for automated assessment of protein structure template quality.
Proteins 2004;57(4):702-10.
2004: Zhang Yang; Skolnick Jeffrey
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
Biophysical journal 2004;87(4):2647-55.
2004: Betancourt Marcos R; Skolnick Jeffrey
Local propensities and statistical potentials of backbone dihedral angles in proteins.
Journal of molecular biology 2004;342(2):635-49.
2004: Li Wei; Zhang Yang; Skolnick Jeffrey
Application of sparse NMR restraints to large-scale protein structure prediction.
Biophysical journal 2004;87(2):1241-8.
2004: Skolnick Jeffrey; Kihara Daisuke; Zhang Yang
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm.
Proteins 2004;56(3):502-18.
2004: Zhang Yang; Skolnick Jeffrey
Automated structure prediction of weakly homologous proteins on a genomic scale.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(20):7594-9.
2004: Kihara Daisuke; Skolnick Jeffrey
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q.
Proteins 2004;55(2):464-73.
2004: Arakaki Adrian K; Zhang Yang; Skolnick Jeffrey
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
Bioinformatics (Oxford, England) 2004;20(7):1087-96.
2004: Zhang Yang; Skolnick Jeffrey
SPICKER: a clustering approach to identify near-native protein folds.
Journal of computational chemistry 2004;25(6):865-71.
2004: Tian Weidong; Arakaki Adrian K; Skolnick Jeffrey
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.
Nucleic acids research 2004;32(21):6226-39.
2003: Lu Hui; Skolnick Jeffrey
Application of statistical potentials to protein structure refinement from low resolution ab initio models.
Biopolymers 2003;70(4):575-84.
2003: Haliloglu Turkan; Kolinski Andrzej; Skolnick Jeffrey
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
Biopolymers 2003;70(4):548-62.
2003: Kihara Daisuke; Skolnick Jeffrey
The PDB is a covering set of small protein structures.
Journal of molecular biology 2003;334(4):793-802.
2003: Boniecki Michal; Rotkiewicz Piotr; Skolnick Jeffrey; Kolinski Andrzej
Protein fragment reconstruction using various modeling techniques.
Journal of computer-aided molecular design 2003;17(11):725-38.
2003: Kolinski Andrzej; Klein Piotr; Romiszowski Piotr; Skolnick Jeffrey
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model.
Biophysical journal 2003;85(5):3271-8.
2003: Li Wei; Zhang Yang; Kihara Daisuke; Huang Yuanpeng Janet; Zheng Deyou; Montelione Gaetano T; Kolinski Andrzej; Skolnick Jeffrey
TOUCHSTONEX: protein structure prediction with sparse NMR data.
Proteins 2003;53(2):290-306.
2003: Tian Weidong; Skolnick Jeffrey
How well is enzyme function conserved as a function of pairwise sequence identity?
Journal of molecular biology 2003;333(4):863-82.
2003: Zhang Yang; Kolinski Andrzej; Skolnick Jeffrey
TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Biophysical journal 2003;85(2):1145-64.
2003: Kolinski Andrzej; Gront Dominik; Pokarowski Piotr; Skolnick Jeffrey
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.
Biopolymers 2003;69(3):399-405.
2003: Lu Long; Arakaki Adrian K; Lu Hui; Skolnick Jeffrey
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.
Genome research 2003;13(6A):1146-54.
2003: Lu Hui; Lu Long; Skolnick Jeffrey
Development of unified statistical potentials describing protein-protein interactions.
Biophysical journal 2003;84(3):1895-901.
2003: Pokarowski Piotr; Kolinski Andrzej; Skolnick Jeffrey
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.
Biophysical journal 2003;84(3):1518-26.
2003: Skolnick Jeffrey; Zhang Yang; Arakaki Adrian K; Kolinski Andrzej; Boniecki Michal; Szilágyi András; Kihara Daisuke
TOUCHSTONE: a unified approach to protein structure prediction.
Proteins 2003;53 Suppl 6():469-79.
2002: Fetrow J S; Giammona A; Kolinski A; Skolnick J
The protein folding problem: a biophysical enigma.
Current pharmaceutical biotechnology 2002;3(4):329-47.
2002: Viñals Jorge; Kolinski Andrzej; Skolnick Jeffrey
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper.
Biophysical journal 2002;83(5):2801-11.
2002: Lu Long; Lu Hui; Skolnick Jeffrey
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
Proteins 2002;49(3):350-64.
2002: Zhang Yang; Kihara Daisuke; Skolnick Jeffrey
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.
Proteins 2002;48(2):192-201.
2002: Kihara Daisuke; Zhang Yang; Lu Hui; Kolinski Andrzej; Skolnick Jeffrey
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5993-8.
2002: Wojciechowski Marek; Skolnick Jeffrey
Docking of small ligands to low-resolution and theoretically predicted receptor structures.
Journal of computational chemistry 2002;23(1):189-97.
2002: Sikorski Andrzej; Kolinski Andrzej; Skolnick Jeffrey
Computer simulations of protein folding with a small number of distance restraints.
Acta biochimica Polonica 2002;49(3):683-92.
2001: Betancourt M R; Skolnick J
Universal similarity measure for comparing protein structures.
Biopolymers 2001;59(5):305-9.
2001: Kihara D; Lu H; Kolinski A; Skolnick J
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(18):10125-30.
2001: Lu H; Skolnick J
A distance-dependent atomic knowledge-based potential for improved protein structure selection.
Proteins 2001;44(3):223-32.
2001: Kolinski A; Betancourt M R; Kihara D; Rotkiewicz P; Skolnick J
Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.
Proteins 2001;44(2):133-49.
2001: Di Gennaro J A; Siew N; Hoffman B T; Zhang L; Skolnick J; Neilson L I; Fetrow J S
Enhanced functional annotation of protein sequences via the use of structural descriptors.
Journal of structural biology 2001;134(2-3):232-45.
2001: Bukhman Y V; Skolnick J
BioMolQuest: integrated database-based retrieval of protein structural and functional information.
Bioinformatics (Oxford, England) 2001;17(5):468-78.
2001: Fetrow J S; Siew N; Di Gennaro J A; Martinez-Yamout M; Dyson H J; Skolnick J
Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?
Protein science : a publication of the Protein Society 2001;10(5):1005-14.
2001: Skolnick J; Kihara D
Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.
Proteins 2001;42(3):319-31.
2001: Skolnick J; Kolinski A; Kihara D; Betancourt M; Rotkiewicz P; Boniecki M
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
Proteins 2001;Suppl 5():149-56.
2000: Sikorski A; Kolinski A; Skolnick J
Monte Carlo simulation of designed helical proteins.
Acta poloniae pharmaceutica 2000;57 Suppl():119-21.
2000: Ortiz A R; Skolnick J
Sequence evolution and the mechanism of protein folding.
Biophysical journal 2000;79(4):1787-99.
2000: Feig M; Rotkiewicz P; Kolinski A; Skolnick J; Brooks C L
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models.
Proteins 2000;41(1):86-97.
2000: Skolnick J; Fetrow J S; Kolinski A
Structural genomics and its importance for gene function analysis.
Nature biotechnology 2000;18(3):283-7.
2000: Sikorski A; Kolinski A; Skolnick J
Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins.
Proteins 2000;38(1):17-28.
2000: Skolnick J; Kolinski A; Ortiz A
Derivation of protein-specific pair potentials based on weak sequence fragment similarity.
Proteins 2000;38(1):3-16.
2000: Skolnick J; Fetrow J S
From genes to protein structure and function: novel applications of computational approaches in the genomic era.
Trends in biotechnology 2000;18(1):34-9.
2000: Reva B A; Finkelstein A V; Skolnick J
Derivation and testing residue-residue mean-force potentials for use in protein structure recognition.
Methods in molecular biology (Clifton, N.J.) 2000;143():155-74.
1999: Kolinski A; Rotkiewicz P; Ilkowski B; Skolnick J
A method for the improvement of threading-based protein models.
Proteins 1999;37(4):592-610.
1999: Kolinski A; Ilkowski B; Skolnick J
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques.
Biophysical journal 1999;77(6):2942-52.
1999: Finkel'shtein A V; Rykunov D S; Lobanov M Iu; Badretdinov F Ia; Reva B A; Skolnick J; Mirnyi L A; Shakhnovich E I
[When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]
Biofizika 1999;44(6):980-91.
1999: Fetrow J S; Siew N; Skolnick J
Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1999;13(13):1866-74.
1999: Mohanty D; Kolinski A; Skolnick J
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.
Biophysical journal 1999;77(1):54-69.
1999: Mohanty D; Dominy B N; Kolinski A; Brooks C L; Skolnick J
Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper.
Proteins 1999;35(4):447-52.
1999: Zhang B; Rychlewski L; Pawlowski K; Fetrow J S; Skolnick J; Godzik A
From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions.
Protein science : a publication of the Protein Society 1999;8(5):1104-15.
1999: Reva B A; Skolnick J; Finkelstein A V
Averaging interaction energies over homologs improves protein fold recognition in gapless threading.
Proteins 1999;35(3):353-9.
1999: Ortiz A R; Kolinski A; Rotkiewicz P; Ilkowski B; Skolnick J
Ab initio folding of proteins using restraints derived from evolutionary information.
Proteins 1999;Suppl 3():177-85.
1998: Skolnick J; Kolinski A; Ortiz A R
Reduced protein models and their application to the protein folding problem.
Journal of biomolecular structure & dynamics 1998;16(2):381-96.
1998: Fetrow J S; Godzik A; Skolnick J
Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity.
Journal of molecular biology 1998;282(4):703-11.
1998: Kolinski A; Skolnick J
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model.
Proteins 1998;32(4):475-94.
1998: Fetrow J S; Skolnick J
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases.
Journal of molecular biology 1998;281(5):949-68.
1998: Milik M; Sauer D; Brunmark A P; Yuan L; Vitiello A; Jackson M R; Peterson P A; Skolnick J; Glass C A
Application of an artificial neural network to predict specific class I MHC binding peptide sequences.
Nature biotechnology 1998;16(8):753-6.
1998: Sikorski A; Kolinski A; Skolnick J
Computer simulations of de novo designed helical proteins.
Biophysical journal 1998;75(1):92-105.
1998: Zhang L; Skolnick J
What should the Z-score of native protein structures be?
Protein science : a publication of the Protein Society 1998;7(5):1201-7.
1998: Keasar C; Tobi D; Elber R; Skolnick J
Coupling the folding of homologous proteins.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):5880-3.
1998: Ortiz A R; Kolinski A; Skolnick J
Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.
Journal of molecular biology 1998;277(2):419-48.
1998: Ortiz A R; Kolinski A; Skolnick J
Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.
Proteins 1998;30(3):287-94.
1998: Ortiz A R; Kolinski A; Skolnick J
Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(3):1020-5.
1998: Zhang L; Skolnick J
How do potentials derived from structural databases relate to "true" potentials?
Protein science : a publication of the Protein Society 1998;7(1):112-22.
1998: Zhang L; Godzik A; Skolnick J; Fetrow J S
Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family.
Folding & design 1998;3(6):535-48.
1998: Reva B A; Rykunov D S; Finkelstein A V; Skolnick J
Optimization of protein structure on lattices using a self-consistent field approach.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(3):531-8.
1998: Ortiz A R; Kolinski A; Skolnick J
Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998;():377-88.
1998: Reva B A; Finkelstein A V; Skolnick J
What is the probability of a chance prediction of a protein structure with an rmsd of 6 A?
Folding & design 1998;3(2):141-7.
1997: Hu W P; Kolinski A; Skolnick J
Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns.
Proteins 1997;29(4):443-60.
1997: Reva B A; Finkelstein A V; Sanner M; Olson A J; Skolnick J
Recognition of protein structure on coarse lattices with residue-residue energy functions.
Protein engineering 1997;10(10):1123-30.
1997: Hu W P; Godzik A; Skolnick J
Sequence-structure specificity--how does an inverse folding approach work?
Protein engineering 1997;10(4):317-31.
1997: Skolnick J; Jaroszewski L; Kolinski A; Godzik A
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
Protein science : a publication of the Protein Society 1997;6(3):676-88.
1997: Kolinski A; Skolnick J; Godzik A; Hu W P
A method for the prediction of surface "U"-turns and transglobular connections in small proteins.
Proteins 1997;27(2):290-308.
1997: Skolnick J; Kolinski A; Ortiz A R
MONSSTER: a method for folding globular proteins with a small number of distance restraints.
Journal of molecular biology 1997;265(2):217-41.
1997: Kolinski A; Skolnick J
High coordination lattice models of protein structure, dynamics and thermodynamics.
Acta biochimica Polonica 1997;44(3):389-422.
1997: Ortiz A R; Hu W P; Kolinski A; Skolnick J
Method for low resolution prediction of small protein tertiary structure.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1997;():316-27.
1997: Keasar C; Elber R; Skolnick J
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction.
Folding & design 1997;2(4):247-59.
1996: Kolinski A; Galazka W; Skolnick J
On the origin of the cooperativity of protein folding: implications from model simulations.
Proteins 1996;26(3):271-87.
1996: Hirst J D; Vieth M; Skolnick J; Brooks C L
Predicting leucine zipper structures from sequence.
Protein engineering 1996;9(8):657-62.
1996: DeBolt S E; Skolnick J
Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions.
Protein engineering 1996;9(8):637-55.
1996: Olszewski K A; Kolinski A; Skolnick J
Folding simulations and computer redesign of protein A three-helix bundle motifs.
Proteins 1996;25(3):286-99.
1996: Olszewski K A; Kolinski A; Skolnick J
Does a backwardly read protein sequence have a unique native state?
Protein engineering 1996;9(1):5-14.
1996: Vieth M; Kolinski A; Skolnick J
Method for predicting the state of association of discretized protein models. Application to leucine zippers.
Biochemistry 1996;35(3):955-67.
1996: Vieth M; Kolinski A; Brooks C L; Skolnick J
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():653-62.
1996: Kolinski A; Skolnick J; Godzik A
An algorithm for prediction of structural elements in small proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():446-60.
1995: Godzik A; Kolinski A; Skolnick J
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets.
Protein science : a publication of the Protein Society 1995;4(10):2107-17.
1995: Milik M; Skolnick J
A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes.
Biophysical journal 1995;69(4):1382-6.
1995: Vieth M; Kolinski A; Brooks C L; Skolnick J
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.
Journal of molecular biology 1995;251(3):448-67.
1995: Milik M; Kolinski A; Skolnick J
Neural network system for the evaluation of side-chain packing in protein structures.
Protein engineering 1995;8(3):225-36.
1994: Godzik A; Skolnick J
Flexible algorithm for direct multiple alignment of protein structures and sequences.
Computer applications in the biosciences : CABIOS 1994;10(6):587-96.
1994: Kolinski A; Skolnick J
Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
Proteins 1994;18(4):353-66.
1994: Kolinski A; Skolnick J
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
Proteins 1994;18(4):338-52.
1994: Vieth M; Kolinski A; Brooks C L; Skolnick J
Prediction of the folding pathways and structure of the GCN4 leucine zipper.
Journal of molecular biology 1994;237(4):361-7.
1993: Godzik A; Skolnick J; Kolinski A
Regularities in interaction patterns of globular proteins.
Protein engineering 1993;6(8):801-10.
1993: Godzik A; Kolinski A; Skolnick J
De novo and inverse folding predictions of protein structure and dynamics.
Journal of computer-aided molecular design 1993;7(4):397-438.
1993: Skolnick J; Kolinski A; Brooks C L; Godzik A; Rey A
A method for predicting protein structure from sequence.
Current biology : CB 1993;3(7):414-23.
1993: Rey A; Skolnick J
Computer modeling and folding of four-helix bundles.
Proteins 1993;16(1):8-28.
1993: Skolnick J; Kolinski A; Godzik A
From independent modules to molten globules: observations on the nature of protein folding intermediates.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(6):2099-100.
1993: Milik M; Skolnick J
Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model.
Proteins 1993;15(1):10-25.
1992: Godzik A; Skolnick J
Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(24):12098-102.
1992: Milik M; Skolnick J
Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(20):9391-5.
1992: Godzik A; Kolinski A; Skolnick J
Topology fingerprint approach to the inverse protein folding problem.
Journal of molecular biology 1992;227(1):227-38.
1992: Godzik A; Skolnick J; Kolinski A
Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(7):2629-33.
1992: Vieth M; Kolinski A; Skolnick J; Sikorski A
Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing.
Acta biochimica Polonica 1992;39(4):369-92.
1991: Skolnick J; Kolinski A
Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.
Journal of molecular biology 1991;221(2):499-531.
1990: Sikorski A; Skolnick J
Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels.
Journal of molecular biology 1990;215(1):183-98.
1990: Sikorski A; Skolnick J
Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs.
Journal of molecular biology 1990;212(4):819-36.
1990: Skolnick J; Kolinski A
Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins.
Journal of molecular biology 1990;212(4):787-817.
1989: Sikorski A; Skolnick J
Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle.
Biopolymers 1989;28(6):1097-113.
1989: Skolnick J; Kolinski A; Yaris R
Monte Carlo studies on equilibrium globular protein folding. II. Beta-barrel globular protein models.
Biopolymers 1989;28(6):1059-95.
1989: Sikorski A; Skolnick J
Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(8):2668-72.
1989: Skolnick J; Kolinski A; Yaris R
Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(4):1229-33.
1989: Skolnick J; Kolinski A
Computer simulations of globular protein folding and tertiary structure.
Annual review of physical chemistry 1989;40():207-35.
1988: Skolnick J; Kolinski A; Yaris R
Monte Carlo simulations of the folding of beta-barrel globular proteins.
Proceedings of the National Academy of Sciences of the United States of America 1988;85(14):5057-61.
1988: Holtzer A; Skolnick J
Application of the augmented theory of alpha-helix-to-random-coil transitions of two-chain, coiled coils to extant data on synthetic, tropomyosin-analog peptides.
Biopolymers 1988;27(1):87-96.
1987: Kolinski A; Skolnick J; Yaris R
Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteins.
Biopolymers 1987;26(6):937-62.
1987: Skolnick J
Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction.
Biophysical journal 1987;51(2):227-43.
1986: Duffy P; Skolnick J; Holtzer A
A theoretical model simulating the anomalous concentration dependence of the equilibrium thermal unfolding curve of noncrosslinked tropomyosin.
Biochemical and biophysical research communications 1986;141(1):394-8.
1986: Skolnick J; Holtzer A
Alpha-helix-to-random-coil transitions of two-chain, coiled coils: a theoretical model for the "pretransition" in cysteine-190-cross-linked tropomyosin.
Biochemistry 1986;25(20):6192-202.
1986: Kolinski A; Skolnick J; Yaris R
Monte Carlo simulations on an equilibrium globular protein folding model.
Proceedings of the National Academy of Sciences of the United States of America 1986;83(19):7267-71.
1985: Skolnick J
Role of topological constraints in the all-or-none transition of a globular protein model: theory of the helix-coil transition in doubly crosslinked, coiled coils.
Biochemical and biophysical research communications 1985;129(3):848-53.

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