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Jeffrey Skolnick

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Protein Folding

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TOP 3
Mu Gao; Jeffrey Skolnick
APoc: large-scale identification of similar protein pockets.
Hongyi Zhou; Jeffrey Skolnick
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.
Tadashi Ando; Jeffrey Skolnick
On the importance of hydrodynamic interactions in lipid membrane formation.

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All Publications

2013: Mu Gao; Jeffrey Skolnick
APoc: large-scale identification of similar protein pockets.
Bioinformatics (Oxford, England) 2013;29(5):597-604.
2013: Hongyi Zhou; Jeffrey Skolnick
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.
Journal of chemical information and modeling 2013;53(1):230-40.
2013: Tadashi Ando; Jeffrey Skolnick
On the importance of hydrodynamic interactions in lipid membrane formation.
Biophysical journal 2013;104(1):96-105.
2013: Sunhwan Jo; Hui Sun Lee; Jeffrey Skolnick; Wonpil Im
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.
PLoS computational biology 2013;9(3):e1002946.
2012: Narendra Kumar; Jeffrey Skolnick
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes.
Bioinformatics (Oxford, England) 2012;28(20):2687-8.
2012: Tadashi Ando; Edmond Chow; Yousef Saad; Jeffrey Skolnick
Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations.
The Journal of chemical physics 2012;137(6):064106.
2012: Jeffrey Skolnick; Hongyi Zhou; Michal Brylinski
Further evidence for the likely completeness of the library of solved single domain protein structures.
The journal of physical chemistry. B 2012;116(23):6654-64.
2012: Hongyi Zhou; Jeffrey Skolnick
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.
Molecular pharmaceutics 2012;9(6):1775-84.
2012: Mu Gao; Jeffrey Skolnick
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(10):3784-9.
2011: Hongyi Zhou; Jeffrey Skolnick
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.
Biophysical journal 2011;101(8):2043-52.
2011: Michal Brylinski; Mu Gao; Jeffrey Skolnick
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function.
Physical chemistry chemical physics : PCCP 2011;13(38):17044-55.
2011: Mu Gao; Jeffrey Skolnick
New benchmark metrics for protein-protein docking methods.
Proteins 2011;79(5):1623-34.
2011: Jeffrey Skolnick; Richard Friesner
Theory and simulation. Editorial overview.
Current opinion in structural biology 2011;21(2):147-9.
2011: Michal Brylinski; Jeffrey Skolnick
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level.
Proteins 2011;79(3):735-51.
2011: Michal Brylinski; Seung Yup Lee; Hongyi Zhou; Jeffrey Skolnick
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.
Journal of structural biology 2011;173(3):558-69.
2010: Mu Gao; Jeffrey Skolnick
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(52):22517-22.
2010: Michal Brylinski; Jeffrey Skolnick
Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach.
Molecular pharmaceutics 2010;7(6):2324-33.
2010: Seung Yup Lee; Jeffrey Skolnick
TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets.
Biophysical journal 2010;99(9):3066-75.
2010: Tadashi Ando; Jeffrey Skolnick
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(43):18457-62.
2010: Michal Brylinski; Jeffrey Skolnick
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening.
Journal of chemical information and modeling 2010;50(10):1839-54.
2010: Shashi B Pandit; Jeffrey Skolnick
TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates.
Proteins 2010;78(13):2769-80.
2010: Mu Gao; Jeffrey Skolnick
iAlign: a method for the structural comparison of protein-protein interfaces.
Bioinformatics (Oxford, England) 2010;26(18):2259-65.
2010: Hongyi Zhou; Jeffrey Skolnick
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons.
Proteins 2010;78(9):2041-8.
2010: Michal Brylinski; Jeffrey Skolnick
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.
Journal of computational chemistry 2010;31(5):1093-105.
2010: Shashi B Pandit; Michal Brylinski; Hongyi Zhou; Mu Gao; Adrian Arakaki; Jeffrey Skolnick
PSiFR: an integrated resource for prediction of protein structure and function.
Bioinformatics (Oxford, England) 2010;26(5):687-8.
2010: Michal Brylinski; Jeffrey Skolnick
Comparison of structure-based and threading-based approaches to protein functional annotation.
Proteins 2010;78(1):118-34.
2009: Mu Gao; Jeffrey Skolnick
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: Jeffrey Skolnick; Adrian Arakaki; Seung Yup Lee; Michal Brylinski
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: Jeffrey Skolnick; Michal Brylinski
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
Briefings in bioinformatics 2009;10(4):378-91.
2009: Michal Brylinski; Jeffrey Skolnick
FINDSITE: a threading-based approach to ligand homology modeling.
PLoS computational biology 2009;5(6):e1000405.
2009: Jeffrey Skolnick; Richard A Friesner
Editorial overview.
Current opinion in structural biology 2009;19(2):117-9.
2009: Hongyi Zhou; Jeffrey Skolnick
Protein structure prediction by pro-Sp3-TASSER.
Biophysical journal 2009;96(6):2119-27.
2009: Mu Gao; Jeffrey Skolnick
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.
PLoS computational biology 2009;5(3):e1000341.
2009: Hongyi Zhou; Shashi B Pandit; Jeffrey Skolnick
Performance of the Pro-sp3-TASSER server in CASP8.
Proteins 2009;77 Suppl 9():123-7.
2009: Adrian K Arakaki; Ying Huang; Jeffrey Skolnick
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.
BMC bioinformatics 2009;10():107.
2008: Adrian Arakaki; Jeffrey Skolnick; John F McDonald
Marker metabolites can be therapeutic targets as well.
Nature 2008;456(7221):443.
2008: Seung Yup Lee; Jeffrey Skolnick
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: Michal Brylinski; Jeffrey Skolnick
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints.
Journal of computational chemistry 2008;29(10):1574-88.
2008: Piotr Rotkiewicz; Jeffrey Skolnick
Fast procedure for reconstruction of full-atom protein models from reduced representations.
Journal of computational chemistry 2008;29(9):1460-5.
2008: Mu Gao; Jeffrey Skolnick
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
Nucleic acids research 2008;36(12):3978-92.
2008: J A Somarelli; S Y Lee; Jeffrey Skolnick; Rene J Herrera
Structure-based classification of 45 FK506-binding proteins.
Proteins 2008;72(1):197-208.
2008: Anna Jagielska; Liliana Wroblewska; Jeffrey Skolnick
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: RyangGuk Kim; Jeffrey Skolnick
Assessment of programs for ligand binding affinity prediction.
Journal of computational chemistry 2008;29(8):1316-31.
2008: Hongyi Zhou; Jeffrey Skolnick
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential.
Proteins 2008;71(3):1211-8.
2008: Liliana Wroblewska; Anna Jagielska; Jeffrey Skolnick
Development of a physics-based force field for the scoring and refinement of protein models.
Biophysical journal 2008;94(8):3227-40.
2008: Huiling Chen; Jeffrey Skolnick
M-TASSER: an algorithm for protein quaternary structure prediction.
Biophysical journal 2008;94(3):918-28.
2008: Michal Brylinski; Jeffrey Skolnick
What is the relationship between the global structures of apo and holo proteins?
Proteins 2008;70(2):363-77.
2008: Michal Brylinski; Jeffrey Skolnick
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: Shashi B Pandit; Jeffrey Skolnick
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.
BMC bioinformatics 2008;9():531.
2008: Adrian Arakaki; Roman Mezencev; Nathan Bowen; Ying Huang; John F McDonald; Jeffrey Skolnick
Identification of metabolites with anticancer properties by computational metabolomics.
Molecular cancer 2008;7():57.
2008: Sara H Thomas; Ryan D Wagner; Adrian Arakaki; Jeffrey Skolnick; John R Kirby; Lawrence J Shimkets; Robert A Sanford; Frank E Loeffler
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: Robert J Martinez; Melanie J Beazley; Martial Taillefert; Adrian Arakaki; Jeffrey Skolnick; Patricia A Sobecky
Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils.
Environmental microbiology 2007;9(12):3122-33.
2007: Hongyi Zhou; Jeffrey Skolnick
Ab initio protein structure prediction using chunk-TASSER.
Biophysical journal 2007;93(5):1510-8.
2007: Liliana Wroblewska; Jeffrey Skolnick
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: Anna Jagielska; Jeffrey Skolnick
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: Seung Yup Lee; Jeffrey Skolnick
Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions.
Proteins 2007;68(1):39-47.
2007: Jose M Borreguero; Jeffrey Skolnick
Benchmarking of TASSER in the ab initio limit.
Proteins 2007;68(1):48-56.
2007: Zhaofeng Ding; Huachun Wang; Xiangyang Liang; Erin R Morris; Fabio Gallazzi; Shashi Pandit; Jeffrey Skolnick; John C Walker; Steven R Van Doren
Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase.
Biochemistry 2007;46(10):2684-96.
2007: Hongyi Zhou; Shashi B Pandit; Seung Yup Lee; Jose M Borreguero; Huiling Chen; Liliana Wroblewska; Jeffrey Skolnick
Analysis of TASSER-based CASP7 protein structure prediction results.
Proteins 2007;69 Suppl 8():90-7.
2007: Sitao Wu; Jeffrey Skolnick; Yang Zhang
Ab initio modeling of small proteins by iterative TASSER simulations.
BMC biology 2007;5():17.
2007: Jae Shick Yang; William W Chen; Jeffrey Skolnick; Eugene I Shakhnovich
All-atom ab initio folding of a diverse set of proteins.
Structure (London, England : 1993) 2007;15(1):53-63.
2006: Shashi B Pandit; Yang Zhang; Jeffrey Skolnick
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal 2006;91(11):4180-90.
2006: Vera Grimm; Yang Zhang; Jeffrey Skolnick
Benchmarking of dimeric threading and structure refinement.
Proteins 2006;63(3):457-65.
2006: Seung Yup Lee; Yang Zhang; Jeffrey Skolnick
TASSER-based refinement of NMR structures.
Proteins 2006;63(3):451-6.
2006: András Szilágyi; Jeffrey Skolnick
Efficient prediction of nucleic acid binding function from low-resolution protein structures.
Journal of molecular biology 2006;358(3):922-33.
2006: Jeffrey Skolnick
In quest of an empirical potential for protein structure prediction.
Current opinion in structural biology 2006;16(2):166-71.
2006: Yang Zhang; Isaac A Hubner; Adrian Arakaki; Eugene Shakhnovich; Jeffrey Skolnick
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: Yang Zhang; Mark E Devries; Jeffrey Skolnick
Structure modeling of all identified G protein-coupled receptors in the human genome.
PLoS computational biology 2006;2(2):e13.
2006: Adrian Arakaki; Weidong Tian; Jeffrey Skolnick
High precision multi-genome scale reannotation of enzyme function by EFICAz.
BMC genomics 2006;7():315.
2005: András Szilágyi; Vera Grimm; Adrian Arakaki; Jeffrey Skolnick
Prediction of physical protein-protein interactions.
Physical biology 2005;2(2):S1-16.
2005: Eckart Bindewald; Jeffrey Skolnick
A scoring function for docking ligands to low-resolution protein structures.
Journal of computational chemistry 2005;26(4):374-83.
2005: Jeffrey Skolnick
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: Yang Zhang; Jeffrey Skolnick
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: Yang Zhang; Adrian Arakaki; Jeffrey Skolnick
TASSER: an automated method for the prediction of protein tertiary structures in CASP6.
Proteins 2005;61 Suppl 7():91-8.
2005: Yang Zhang; Jeffrey Skolnick
TM-align: a protein structure alignment algorithm based on the TM-score.
Nucleic acids research 2005;33(7):2302-9.
2004: Yang Zhang; Jeffrey Skolnick
Scoring function for automated assessment of protein structure template quality.
Proteins 2004;57(4):702-10.
2004: Yang Zhang; Jeffrey Skolnick
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
Biophysical journal 2004;87(4):2647-55.
2004: Marcos R Betancourt; Jeffrey Skolnick
Local propensities and statistical potentials of backbone dihedral angles in proteins.
Journal of molecular biology 2004;342(2):635-49.
2004: Jeffrey Skolnick; Daisuke Kihara; Yang Zhang
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm.
Proteins 2004;56(3):502-18.
2004: Wei Li; Yang Zhang; Jeffrey Skolnick
Application of sparse NMR restraints to large-scale protein structure prediction.
Biophysical journal 2004;87(2):1241-8.
2004: Yang Zhang; Jeffrey Skolnick
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: Daisuke Kihara; Jeffrey Skolnick
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q.
Proteins 2004;55(2):464-73.
2004: Adrian Arakaki; Yang Zhang; Jeffrey Skolnick
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
Bioinformatics (Oxford, England) 2004;20(7):1087-96.
2004: Yang Zhang; Jeffrey Skolnick
SPICKER: a clustering approach to identify near-native protein folds.
Journal of computational chemistry 2004;25(6):865-71.
2004: Weidong Tian; Adrian Arakaki; Jeffrey Skolnick
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.
Nucleic acids research 2004;32(21):6226-39.
2003: Daisuke Kihara; Jeffrey Skolnick
The PDB is a covering set of small protein structures.
Journal of molecular biology 2003;334(4):793-802.
2003: Hui Lu; Jeffrey Skolnick
Application of statistical potentials to protein structure refinement from low resolution ab initio models.
Biopolymers 2003;70(4):575-84.
2003: Turkan Haliloglu; Andrzej Kolinski; Jeffrey Skolnick
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
Biopolymers 2003;70(4):548-62.
2003: Michal Boniecki; Piotr Rotkiewicz; Jeffrey Skolnick; Andrzej Kolinski
Protein fragment reconstruction using various modeling techniques.
Journal of computer-aided molecular design 2003;17(11):725-38.
2003: Andrzej Kolinski; Piotr Klein; Piotr Romiszowski; Jeffrey Skolnick
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model.
Biophysical journal 2003;85(5):3271-8.
2003: Wei Li; Yang Zhang; Daisuke Kihara; Yuanpeng J Huang; Deyou Zheng; Gaetano T Montelione; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONEX: protein structure prediction with sparse NMR data.
Proteins 2003;53(2):290-306.
2003: Weidong Tian; Jeffrey Skolnick
How well is enzyme function conserved as a function of pairwise sequence identity?
Journal of molecular biology 2003;333(4):863-82.
2003: Yang Zhang; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Biophysical journal 2003;85(2):1145-64.
2003: Andrzej Kolinski; Dominik Gront; Piotr Pokarowski; Jeffrey Skolnick
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.
Biopolymers 2003;69(3):399-405.
2003: Long Lu; Adrian Arakaki; Hui Lu; Jeffrey Skolnick
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: Hui Lu; Long Lu; Jeffrey Skolnick
Development of unified statistical potentials describing protein-protein interactions.
Biophysical journal 2003;84(3):1895-901.
2003: Piotr Pokarowski; Andrzej Kolinski; Jeffrey Skolnick
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: Jeffrey Skolnick; Yang Zhang; Adrian Arakaki; Andrzej Kolinski; Michal Boniecki; András Szilágyi; Daisuke Kihara
TOUCHSTONE: a unified approach to protein structure prediction.
Proteins 2003;53 Suppl 6():469-79.
2002: J S Fetrow; A Giammona; A Kolinski; Jeffrey Skolnick
The protein folding problem: a biophysical enigma.
Current pharmaceutical biotechnology 2002;3(4):329-47.
2002: Long Lu; Hui Lu; Jeffrey Skolnick
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
Proteins 2002;49(3):350-64.
2002: Jorge Viñals; Andrzej Kolinski; Jeffrey Skolnick
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: Yang Zhang; Daisuke Kihara; Jeffrey Skolnick
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.
Proteins 2002;48(2):192-201.
2002: Daisuke Kihara; Yang Zhang; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
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: Marek Wojciechowski; Jeffrey Skolnick
Docking of small ligands to low-resolution and theoretically predicted receptor structures.
Journal of computational chemistry 2002;23(1):189-97.
2002: Andrzej Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of protein folding with a small number of distance restraints.
Acta biochimica Polonica 2002;49(3):683-92.
2001: M R Betancourt; Jeffrey Skolnick
Universal similarity measure for comparing protein structures.
Biopolymers 2001;59(5):305-9.
2001: Daisuke Kihara; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
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: Hui Lu; Jeffrey Skolnick
A distance-dependent atomic knowledge-based potential for improved protein structure selection.
Proteins 2001;44(3):223-32.
2001: Andrzej Kolinski; M R Betancourt; Daisuke Kihara; Piotr Rotkiewicz; Jeffrey Skolnick
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: Jeannine A Di Gennaro; N Siew; Brian T Hoffman; L Zhang; Jeffrey Skolnick; L I Neilson; Jacquelyn S Fetrow
Enhanced functional annotation of protein sequences via the use of structural descriptors.
Journal of structural biology 2001;134(2-3):232-45.
2001: Y V Bukhman; Jeffrey Skolnick
BioMolQuest: integrated database-based retrieval of protein structural and functional information.
Bioinformatics (Oxford, England) 2001;17(5):468-78.
2001: Jacquelyn S Fetrow; N Siew; Jeannine A Di Gennaro; Maria A Martinez-Yamout; H Jane Dyson; Jeffrey Skolnick
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: Jeffrey Skolnick; D Kihara
Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.
Proteins 2001;42(3):319-31.
2001: Jeffrey Skolnick; Andrzej Kolinski; Daisuke Kihara; M Betancourt; Piotr Rotkiewicz; Michal Boniecki
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
Proteins 2001;Suppl 5():149-56.
2000: Andrzej Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulation of designed helical proteins.
Acta poloniae pharmaceutica 2000;57 Suppl():119-21.
2000: AR Ortiz; Jeffrey Skolnick
Sequence evolution and the mechanism of protein folding.
Biophysical journal 2000;79(4):1787-99.
2000: Michael Feig; Piotr Rotkiewicz; Andrzej Kolinski; Jeffrey Skolnick; Charles L Brooks
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models.
Proteins 2000;41(1):86-97.
2000: Jeffrey Skolnick; J S Fetrow; A Kolinski
Structural genomics and its importance for gene function analysis.
Nature biotechnology 2000;18(3):283-7.
2000: BA Reva; Alexei V Finkelstein; Jeffrey Skolnick
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.
2000: A Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins.
Proteins 2000;38(1):17-28.
2000: Jeffrey Skolnick; A Kolinski; A Ortiz
Derivation of protein-specific pair potentials based on weak sequence fragment similarity.
Proteins 2000;38(1):3-16.
2000: Jeffrey Skolnick; J S Fetrow
From genes to protein structure and function: novel applications of computational approaches in the genomic era.
Trends in biotechnology 2000;18(1):34-9.
1999: Andrzej Kolinski; Piotr Rotkiewicz; B Ilkowski; Jeffrey Skolnick
A method for the improvement of threading-based protein models.
Proteins 1999;37(4):592-610.
1999: Andrzej Kolinski; B Ilkowski; Jeffrey Skolnick
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques.
Biophysical journal 1999;77(6):2942-52.
1999: A V Finkel'shteĭn; DS Rykunov; MIu Lobanov; F Ia Badretdinov; BA Reva; Jeffrey Skolnick; L A Mirnyĭ; E I Shakhnovich
[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: Jacquelyn S Fetrow; N Siew; Jeffrey Skolnick
Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1999;13(13):1866-74.
1999: DEBASISA MOHANTY; Andrzej Kolinski; Jeffrey Skolnick
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.
Biophysical journal 1999;77(1):54-69.
1999: DEBASISA MOHANTY; Brian Dominy; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper.
Proteins 1999;35(4):447-52.
1999: BA Reva; Jeffrey Skolnick; Alexei V Finkelstein
Averaging interaction energies over homologs improves protein fold recognition in gapless threading.
Proteins 1999;35(3):353-9.
1999: B Zhang; Leszek Rychlewski; K Pawłowski; Jacquelyn S Fetrow; Jeffrey Skolnick; Adam Godzik
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: AR Ortiz; Andrzej Kolinski; Piotr Rotkiewicz; B Ilkowski; Jeffrey Skolnick
Ab initio folding of proteins using restraints derived from evolutionary information.
Proteins 1999;Suppl 3():177-85.
1998: Jacquelyn S Fetrow; Adam Godzik; Jeffrey Skolnick
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: Jeffrey Skolnick; Andrzej Kolinski; AR Ortiz
Reduced protein models and their application to the protein folding problem.
Journal of biomolecular structure & dynamics 1998;16(2):381-96.
1998: J S Fetrow; Jeffrey Skolnick
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: Andrzej Kolinski; Jeffrey Skolnick
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model.
Proteins 1998;32(4):475-94.
1998: Mariusz Milik; D Sauer; A P Brunmark; L Yuan; Antonella Vitiello; MR Jackson; PA Peterson; Jeffrey Skolnick; C A Glass
Application of an artificial neural network to predict specific class I MHC binding peptide sequences.
Nature biotechnology 1998;16(8):753-6.
1998: A Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of de novo designed helical proteins.
Biophysical journal 1998;75(1):92-105.
1998: C Keasar; Dror Tobi; Ron Elber; Jeffrey Skolnick
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: L Zhang; Jeffrey Skolnick
What should the Z-score of native protein structures be?
Protein science : a publication of the Protein Society 1998;7(5):1201-7.
1998: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
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: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
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: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
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: L Zhang; Adam Godzik; Jeffrey Skolnick; J S Fetrow
Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family.
Folding & design 1998;3(6):535-48.
1998: BA Reva; DS Rykunov; Alexei V Finkelstein; Jeffrey Skolnick
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: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
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: BA Reva; Alexei V Finkelstein; Jeffrey Skolnick
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.
1998: L Zhang; Jeffrey Skolnick
How do potentials derived from structural databases relate to "true" potentials?
Protein science : a publication of the Protein Society 1998;7(1):112-22.
1997: WP Hu; Andrzej Kolinski; Jeffrey Skolnick
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: BA Reva; Alexei V Finkelstein; Michel F Sanner; Arthur J Olson; Jeffrey Skolnick
Recognition of protein structure on coarse lattices with residue-residue energy functions.
Protein engineering 1997;10(10):1123-30.
1997: WP Hu; A Godzik; Jeffrey Skolnick
Sequence-structure specificity--how does an inverse folding approach work?
Protein engineering 1997;10(4):317-31.
1997: Jeffrey Skolnick; Lukasz Jaroszewski; A Kolinski; Adam Godzik
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: Andrzej Kolinski; Jeffrey Skolnick; A Godzik; WP Hu
A method for the prediction of surface "U"-turns and transglobular connections in small proteins.
Proteins 1997;27(2):290-308.
1997: Jeffrey Skolnick; Andrzej Kolinski; AR Ortiz
MONSSTER: a method for folding globular proteins with a small number of distance restraints.
Journal of molecular biology 1997;265(2):217-41.
1997: A Koliński; Jeffrey Skolnick
High coordination lattice models of protein structure, dynamics and thermodynamics.
Acta biochimica Polonica 1997;44(3):389-422.
1997: AR Ortiz; WP Hu; Andrzej Kolinski; Jeffrey Skolnick
Method for low resolution prediction of small protein tertiary structure.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1997;():316-27.
1997: C Keasar; Ron Elber; Jeffrey Skolnick
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction.
Folding & design 1997;2(4):247-59.
1996: Andrzej Kolinski; W Galazka; Jeffrey Skolnick
On the origin of the cooperativity of protein folding: implications from model simulations.
Proteins 1996;26(3):271-87.
1996: J D Hirst; M Vieth; Jeffrey Skolnick; Charles L Brooks
Predicting leucine zipper structures from sequence.
Protein engineering 1996;9(8):657-62.
1996: S E DeBolt; Jeffrey Skolnick
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: K A Olszewski; Andrzej Kolinski; Jeffrey Skolnick
Folding simulations and computer redesign of protein A three-helix bundle motifs.
Proteins 1996;25(3):286-99.
1996: M Vieth; Andrzej Kolinski; Jeffrey Skolnick
Method for predicting the state of association of discretized protein models. Application to leucine zippers.
Biochemistry 1996;35(3):955-67.
1996: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
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: Andrzej Kolinski; Jeffrey Skolnick; Adam Godzik
An algorithm for prediction of structural elements in small proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():446-60.
1996: K A Olszewski; Andrzej Kolinski; Jeffrey Skolnick
Does a backwardly read protein sequence have a unique native state?
Protein engineering 1996;9(1):5-14.
1995: Adam Godzik; A Koliński; Jeffrey Skolnick
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: Mariusz Milik; Jeffrey Skolnick
A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes.
Biophysical journal 1995;69(4):1382-6.
1995: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
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: Mariusz Milik; A Kolinski; Jeffrey Skolnick
Neural network system for the evaluation of side-chain packing in protein structures.
Protein engineering 1995;8(3):225-36.
1994: Adam Godzik; Jeffrey Skolnick
Flexible algorithm for direct multiple alignment of protein structures and sequences.
Computer applications in the biosciences : CABIOS 1994;10(6):587-96.
1994: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of the folding pathways and structure of the GCN4 leucine zipper.
Journal of molecular biology 1994;237(4):361-7.
1994: Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
Proteins 1994;18(4):353-66.
1994: Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
Proteins 1994;18(4):338-52.
1993: Adam Godzik; Jeffrey Skolnick; Andrzej Kolinski
Regularities in interaction patterns of globular proteins.
Protein engineering 1993;6(8):801-10.
1993: Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick
De novo and inverse folding predictions of protein structure and dynamics.
Journal of computer-aided molecular design 1993;7(4):397-438.
1993: Jeffrey Skolnick; Andrzej Kolinski; C L Brooks; Adam Godzik; A Rey
A method for predicting protein structure from sequence.
Current biology : CB 1993;3(7):414-23.
1993: A Rey; Jeffrey Skolnick
Computer modeling and folding of four-helix bundles.
Proteins 1993;16(1):8-28.
1993: Jeffrey Skolnick; Andrzej Kolinski; Adam Godzik
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: Mariusz Milik; Jeffrey Skolnick
Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model.
Proteins 1993;15(1):10-25.
1992: Adam Godzik; Jeffrey Skolnick
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: Mariusz Milik; Jeffrey Skolnick
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: Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick
Topology fingerprint approach to the inverse protein folding problem.
Journal of molecular biology 1992;227(1):227-38.
1992: Adam Godzik; Jeffrey Skolnick; Andrzej Kolinski
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: M Vieth; A Koliński; Jeffrey Skolnick; A Sikorski
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: Jeffrey Skolnick; A Kolinski
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: A Sikorski; Jeffrey Skolnick
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: A Sikorski; Jeffrey Skolnick
Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs.
Journal of molecular biology 1990;212(4):819-36.
1990: Jeffrey Skolnick; A Kolinski
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: A Sikorski; Jeffrey Skolnick
Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle.
Biopolymers 1989;28(6):1097-113.
1989: Jeffrey Skolnick; A Kolinski; R Yaris
Monte Carlo studies on equilibrium globular protein folding. II. Beta-barrel globular protein models.
Biopolymers 1989;28(6):1059-95.
1989: A Sikorski; Jeffrey Skolnick
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: Jeffrey Skolnick; A Kolinski; R Yaris
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: Jeffrey Skolnick; A Kolinski
Computer simulations of globular protein folding and tertiary structure.
Annual review of physical chemistry 1989;40():207-35.
1988: Jeffrey Skolnick; A Kolinski; R Yaris
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: A Holtzer; Jeffrey Skolnick
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: A Kolinski; Jeffrey Skolnick; R Yaris
Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteins.
Biopolymers 1987;26(6):937-62.
1987: Jeffrey Skolnick
Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction.
Biophysical journal 1987;51(2):227-43.
1986: P Duffy; Jeffrey Skolnick; A Holtzer
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: Jeffrey Skolnick; A Holtzer
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: A Kolinski; Jeffrey Skolnick; R Yaris
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: Jeffrey Skolnick
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.