Georgia Institute of TechnologyCSSB
Skolnick Lab Logo
2009    
[310]
H. Zhou and J. Skolnick. Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins (submitted).
[309]
J. Skolnick, M. Brylinski and S. Lee. Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected. Proc Natl Acad Science 2009:106(51): E138.
[308]
S. B. Pandit, M. Brylinski, H. Zhou, M. Gao, A. K. Arakaki and J. Skolnick. PSiFR: An integrated resource for prediction of protein structure and function. Bioinformatics (submitted).
[307]
J. Skolnick and M. Brylinski. Novel computational approaches to drug discovery. Proceedings of the International Conference of the Quantum Bio-Informatics Research Center 2009 (accepted). NIHMSID: 165616
[306] PDF M. Brylinski and J. Skolnick. Q-DockLHM: Low-resolution refinement for ligand comparative modeling. Journal of Computational Chemistry 2009:DOI 10.1002/jcc.21395. NIHMSID: 165534
[305] PDF M. Gao and J. 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. PMCID: PMC2770119
[304] PDF J. Skolnick and R. A. Friesner. Theory and simulation. Current Opinion in Structural Biology 2009:19: 117-119. NIHMSID: 115574. PMCID: PMC2692031
[303]
M. Brylinski and J. Skolnick. Comparison of structure- and threading-based approaches to protein functional annotation. Proteins 2009:78(1): 118-134. PMC Journal in progress
[302] PDF J. Skolnick, A. K. Arakaki, S. Lee and M. Brylinski. The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Science 2009:106(37): 15609-15695. PMCID: PMC 2747181
[301] PDF H. Zhou, S. B. Pandit and J. Skolnick. Performance of the Pro-sp3-TASSER Server in CASP8. Proteins 2009:77(S9): 123-127. PMCID: PMC2785221
[300] PDF J. Skolnick and M. Brylinski. FINDSITE: A combined evolution /structure-based approach to protein function prediction. Briefings in Bioinformatics 2009: doi: 10.1093/bib/bbp017 PMCID: PMC2691936
[299]
S. B. Pandit, H. Zhou and J. Skolnick. TASSER-based protein structure prediction, in Protein Structure Prediction: Methods and Algorithms (accepted). NIHMSID: 165620
[298] PDF M. Brylinski and J. Skolnick. FINDSITELHM: A threading-based approach to ligand homology modeling. PLoS Computational Biology 2009:5(6): e1000405. doi:10.1371/journal.pcbi.1000405. PMCID: PMC2685473
[297] PDF A. K. Arakaki, Y. Huang and J. Skolnick. EFICAz2: Enzyme Function Inference by a Combined Approach enhanced by machine learning. BMC Bioinformatics 2009:(10): 107. PMCID: PMC2670841.
2008    
[296] PDF A. K. Arakaki, J. F. McDonald and J. Skolnick. Metabolites could be not only markers but disease treatments. Nature 2008:456(7221): 443. NIHMSID: 165613
[295] PDF M. Gao and J. Skolnick. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PloS Computational Biology. 2009:5(3): e1000341. doi:10.1371/journal.pcbi.1000341. PMCID: PMC2659451
[294] PDF H. Zhou and J. Skolnick. Protein structure prediction by pro-sp3-TASSER. Biophysical Journal 2009. 96(6): p. 2119-27. PMCID: PMC2717286
[293] PDF S.B Pandit and J. Skolnick. Fr-TM-align: A new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics :9:531 (Highly accessed). PMCID: PMC2628391
[292] PDF
 M. Gao and J. Skolnick. DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research 36(12): 3978-3992. PMCID: PMC2475642
[291] PDF
 A. Jagielska, L. Wroblewska and J. Skolnick. Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Science, 105 (24): 8268-8273. PMCID: PMC2448826
[290] PDF
 S. H. Thomas, R. D. Wagner, A. K. Arakaki, J. Skolnick, J. R. Kirby, L. J. Shimkets, R. A. Sanford, and F. E. Löffler. The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-Proteobacteria. PLoSONE 2008:3(5): e2103 PMCID: PMC2330069
[289] PDF
 J. A. Somarelli, S. Lee, J. Skolnick, and R. J. Herrera. Structure-based classification of 45 FK506-binding proteins. Proteins 2008:72(1): 197-208. PMCID: PMC2694576
[288] PDF
 S. Lee and J. Skolnick. Benchmarking of TASSER_2.0: An improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophysical Journal 2008:95(4): 1956-1964. PMCID: PMC2483784
[287]
A. K. Arakaki, R. Mezencev, N. Bowen, Y. Huang, J. McDonald and J. Skolnick. Identification of metabolites with anticancer properties by Computational Metabolomics. Molecular Cancer 2008:7: 57 (Highly accessed). PMCID: PMC2453147
[286] PDF
 P. Rotkiewicz and J. Skolnick. Fast procedure for reconstruction of full-atom protein models from reduced representations. Journal of Computational Chemistry 2008:29(9) 1460-1465. PMCID: PMC2692024
[285] L. Wroblewska, A. Jagielska, and J. Skolnick. Development of a physics-based force field for the scoring and refinement of protein models. Biophysical Journal 2008:94(8): 3227-3240. PMCID: PMC2275715
[284] PDF
 M. Brylinski and J. Skolnick. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. Journal of Computational Chemistry 2008:29(10): 1574-1588. PMCID: PMC2726574
[283] PDF
 M. Brylinski and J. Skolnick. FINDSITE: A threading-based method for ligand-binding site prediction and functional annotation. Proc Natl Acad Science 2008: 105: 129-134.PMCID: PMC2224172
[282] H. Chen and J. Skolnick. M-TASSER: An Algorithm for Protein Quaternary Structure Prediction. Biophysical Journal 2008:94(3): 918-928.PMCID: PMC2186260
2007    
[281] PDF
 H. Zhou and J. Skolnick. Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential. Proteins 2007:71:1211-1218.
[280] PDF
 H. Zhou and J. Skolnick. Ab initio protein structure prediction using chunk-TASSER. Biophysical Journal 2007:93: 1510-1518.
[279] PDF
 H. Zhou, S. B. Pandit, S. Lee, J. Borreguerro, H. Chen, L. Wroblewska and J. Skolnick. Analysis of TASSER based CASP7 protein structure prediction results. Proteins 2007:69(S8): 90-97.
[278] PDF
 R. J. Martinez, M. J. Beazley, M. Taillefert, A. K. Arakaki, J. Skolnick, and P. A. Sobecky. Aerobic Uranium(VI) BioPrecipitation by Metal Resistant Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils. Environmental Microbiology. 2007:9(12):3122-3133
[277] PDF
 R. Kim and J. Skolnick. Assessment of Programs for Ligand Binding Affinity Prediction. Journal of Computational Chemistry 2008:29:1316-1331.PMCID: PMC2702145
[276] PDF
 S. Wu, J. Skolnick, and Y. Zhang. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology 2007:5: 17.
[275]
J. Skolnick. Protein Structure Prediction. The Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0003031.
[274] PDF
 L. Wroblewska and J. 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): 2059-2066.
[273] PDF
 M. Brylinski and J. Skolnick. What is the relationship between the global structures of apo and holo proteins? Proteins Proteins 2007:70(2): 363-377.
[272] PDF
 S. Lee and J. Skolnick. Development and benchmarking of TASSERiter for the iterative improvement of protein structure predictions. Proteins 2007:68: 39-47.
[271] PDF
 Z. Ding, H. Wang, X. Liang, E. Morris, F. Gallazzi, S. B. Pandit, J. Skolnick, J. C. Walker, and S. R. Van Doren. Phosphoprotein and Phosphopeptide Interactions with the FHA Domain from Kinase-Associated Protein Phosphatase. Biochemistry 2007:46(10): 2684-2696.
[270] PDF
 J. Borreguero and J. Skolnick. Benchmarking of TASSER in the ab initio limit. Proteins 2007:68: 48-56.
[269] PDF
 A. Jagielska and J. Skolnick. Origin of intrinsic helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field. Journal of Computational Chemistry 2007:28(10): 1648-1657.
2006    
[268] PDF
 A.K. Arakaki, W. Tian and J. Skolnick. High accuracy multi-genome scale reannotation of enzyme function by EFICAz. BMC genetics 2006:7: 315.
[267] PDF
 J. Skolnick. In quest of an empirical potential for protein structure prediction. Current Opinion in Structural Biology 2006:16: 166-171.
[266] PDF
 S. B. Pandit, Y. Zhang and J. Skolnick. TASSER-Lite: An automated tool for protein comparative modeling. Biophysical Journal 2006:91: 4180-4190.
[265] PDF
 A. Szilagyi and J. Skolnick. Efficient prediction of nucleic acid binding function from low-resolution protein structures. J Mol Biol 2006: 358: 922-933.
[264] PDF
 S. Lee, Y. Zhang and J. Skolnick. TASSER-based refinement of NMR structures. Proteins 2006: 63: 451-456.
[263] PDF
 J. Yang, W. Chen, J. Skolnick and E. Shakhnovich. All-atom ab initio folding of a diverse set of protein structures. Structure 2007:15 53-63.
[262] PDF
 Y. Zhang, I. A. Hubner, A. K. Arakaki, E. Shakhnovich and J. Skolnick. On the origin and completeness of single domain structures. Proc Natl Acad Science 2006:103: 2605-2610.
[261] PDF
 V. Grimm, Y. Zhang and J. Skolnick. Benchmarking of dimeric threading and structure refinement. Proteins 2006:63: 457-465.
[260] PDF
 Y. Zhang, M. E. DeVries, and J. Skolnick. Structure modeling of all identified G protein -coupled receptors in the human genome. PLoS Computational Biology 2006:2(2): 88-99.
2005    
[259] PDF
 Y. Zhang and J. Skolnick. TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005:61(S7): 91-98.
[258] PDF
 Y. Zhang and J. Skolnick. TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 2005:33: 2302-2309.
[257] PDF
 J. Skolnick. Putting the pathway back into protein folding. Proc Natl Acad Science 2005:102(7): 2265-2266.
[256] PDF
 A. Szilagyi, V. Grimm, A. Arakaki and J. Skolnick. Prediction of protein-protein interactions. Physical Biology 2005:(2): S1-S16.
2004    
[255] PDF
 W. Tian, A. Arakaki and J. Skolnick. EFICAz: a comprehensive approach to accurate genome-scale enzyme function inference. Nucleic Acids Research 2004:32: 6226-6239.
[254]
J. Skolnick and Y. Zhang. Protein Structure Prediction II. The Systems Biology Review. Rigoutsos and G. Stephanopoulos, Editors. 2007, Oxford University Press: Oxford; New York. p. 187-218.
[253] PDF
 E. Bindewald and J. Skolnick. A scoring function for docking ligands to low-resolution protein structures. Journal of Computational Chemistry 2005:26: 374-383.
[252] PDF
 Y. Zhang and J. Skolnick. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophysical Journal 2004: 87: 2647-2655.
[251] PDF
 W. Li, Y. Zhang and J. Skolnick. Application of sparse NMR restraints to large-scale protein structure prediction. Biophysical Journal 2004:87: 241-1248.
[250] PDF
 M. Betancourt and J. Skolnick. Local propensities and statistical potentials of backbone dihedral angles in proteins. Journal of Molecular Biology 2004: 342: 635-649.
[249] PDF
 Y. Zhang and J. Skolnick. A scoring function for the automated assessment of protein structure template quality. Proteins 2004:57: 702-710.
[248] PDF
 Y. Zhang and J. Skolnick. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Science 2005:102(4): 1029-1034.
[247] PDF
 Y. Zhang and J. Skolnick. SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem. 2004:25: 865-871.
[246]
J. Skolnick. What practical use is protein structure prediction to drug discovery? BioIt World, Commentary, October 10, 2003.
[245] PDF
 Y. Zhang and J. Skolnick. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Science 2004:101: 7594-7599.
[244] PDF
 A. Arakaki, Y. Zhang and J. Skolnick. Large-scale assessment of the utility of low resolution protein structures for biochemical assignment. Bioinformatics 2004:20: 1087-1096.
[243] PDF
 J. Skolnick, D. Kihara and Y. Zhang. Development and testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004:56: 502-518.
[242] PDF
 D. Kihara and J. Skolnick. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins 2004:55: 464-473.
[241] PDF
 A. Kolinski, D. Gront, P. Pokarowski and J. Skolnick. A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers 2003:69: 339-405.
[240] PDF
 A. Kolinski and J. Skolnick. Reduced models of proteins and their applications. Polymer 2004:45(2): 511-524.
2003    
[239] PDF
 M. Boniecki, P. Rotkiewicz, J. Skolnick and A. Kolinski. Protein fragment reconstruction using various modeling techniques. J. Computer Aided Molecular Design 2003:17: 725-738.
[238] PDF
 W. Tian and J. Skolnick. How well is enzyme function conserved? Journal of Molecular Biology 2003:333: 863-882.
[237]
J. Skolnick, Y. Zhang and A. Kolinski. Ab Initio modeling. Structural genomics and high throughput structural biology. M. Sundsrom, M. Norin and A. Edwards, eds. 2006: 137-162.
[236] PDF
 W. Li, Y. Zhang, D. Kihara, Y. Huang, D. Zheng, G. Montelione, A. Kolinski and J. Skolnick. Touchstonex: Protein structure prediction using sparse NMR data. Proteins 2003:53(2): 290-306.
[235] PDF
 A. Kolinski, P. Klein, P. Romiszowski and J. Skolnick. Unfolding of globular proteins: Monte Carlo dynamics of a realistic reduced model. Biophysical Journal. 2003:85: 3271-3278.
[234] PDF
 L. Lu, A. Arakaki, H. Lu and J. Skolnick. Multimeric threading based prediction of protein interactions on a genomic scale: Application to the Saccharomyces Cerevisiae proteome. Genome Research 2003:13: 1146-1154.
[233] PDF
 Y. Zhang, A. Kolinski and J. Skolnick. Touchstone II: A new approach to ab initio protein structure prediction. Biophysical Journal 2003:85: 1145-1164.
[232] PDF
 J. Skolnick, Y. Zhang, A. Arakaki, M. Betancourt, A. Szilagyi and D. Kihara. Touchstone: A unified approach to protein structure prediction. Proteins CASP5 Special Issue 2003:53: 469-479.
[231] PDF
 D. Kihara and J. Skolnick. The PDB is a covering set of small protein structures. Journal of Molecular Biology 2003:333: 393-802.
2002    
[230] PDF
 H. Lu, L. Lu and J. Skolnick. Development of unified statistical potentials describing protein-protein interactions. Biophysical Journal. 2002:84(3): 1895-901.
[229] PDF
 A. Sikorski, A. Kolinski and J. Skolnick. Computer simulation of protein folding with a small number of distance restraints. Acta Biochimca Polonica 2002:49: 683-692.
[228] PDF
 T. Haliloglu, A. Kolinski and J. Skolnick. Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers 2003:70(4): 548-62.
[227] PDF
 P. Pokarowski, A. Kolinski and J. 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.
[226] PDF
 H. Lu, and J. Skolnick. Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers 2003:70(4): 575-84.
[225] PDF
 J. Viñ, A. Kolinski and J. 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.
[224] PDF
 J. S. Fetrow, A. Giammona, A. Kolinski and J. Skolnick. The protein folding problem: A biophysical enigma. Current Pharmaceutical Biotechnology 2002:3(4): 329-47.
[223] PDF
 Y. Zhang, D. Kihara, J. Skolnick. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002:48: 192-201.
[222] PDF
 L. Lu, H. Lu and J. Skolnick. MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002:49: 350-64.
[221] PDF
 D. Kihara, Y. Zhang, A. Kolinski and J. Skolnick. Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome. Proc Natl Acad Sci. 2002:30: 5993-5998.
2001    
[220] PDF
 J. Skolnick and A. Kolinski. Computational studies of protein folding. CISE 2001:3: 40-48.
[219] PDF
 Y. Zhang and J. Skolnick. Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures. J Chem Phys. 2001:115: 5027-5032.
[218] PDF
 D. Kihara, H. Lu, A. Kolinski and J. Skolnick. TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci. 2001:98(18): 10125-10130.
[217] PDF
 M. Wojciechowski and J. Skolnick. Docking of small ligands to low-resolution and theoretically predicted receptor structures. Journal of Computational Physics Special Issue 2002:23: 189-197.
[216]
A. Kolinski, P. Rotkiewicz and J. Skolnick. Structure of proteins: New approach to molecular modeling. Polish J. Chem. 2000:75: 587-599.
[215] PDF
 J. Skolnick, A. Kolinski, D. Kihara, M.R. Betancourt, P. Rotkiewicz and M. Boniecki. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins Special Issue 2001:5: 149-156.
[214] PDF
 M.R. Betancourt, J. Skolnick. Universal similarity measure for comparing protein structures. Biopolymers. 2001:59: 305-309.
[213] PDF
 J. Di Gennaro, N. Siew, B. Hoffman, L. Zhang, J. Skolnick, L. Neilson and J. Fetrow. Enhanced functional annotation of protein sequences via the use of structural descriptors. Journal of Structural Biology 2001:134: 232-245.
[212] PDF
 D. Gront, A. Kolinski and J. Skolnick. A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics. Journal of Computational Physics 2001:115(3): 1569-1574.
[211] PDF
 A. Kolinski, M.R. Betancourt, D. Kihara, P. Rotkiewicz and J. Skolnick. Generalized Comparative Modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001:44: 133-149.
[210] PDF
 H. Lu and J. Skolnick. A distance-dependent atomic knowledge-based potential for protein structure selection. Proteins 2001:44: 223-32.
[209]
J. Skolnick and A. Kolinski. A unified approach to the prediction of protein structure and function. Advances in Chemical Physics 2002:120: 131-192.
[208] PDF
 Y. Bukhman and J. Skolnick. BioMolQuest: A new search engine for the integrated database-based retrieval of protein structural and functional information. Bioinformatics. 2001:17(5): 468-478.
[207] PDF
 M. Betancourt and J.Skolnick. Finding the needle in a haystack: Educing native folds from ambiguous ab initio protein structure prediction. J. Comput. Chem. 2001:22(3): 339-353.
[206]
A.V. Finkelstein, D.S. Rykunov, M. Yu. Lobanov, A. Ya, Badretdinov, B.A. Reva, J. Skolnick, L.A. Mirny and E.I. Shakhnovich. Overcoming the crudeness of energy estimates in protein 3D structure prediction by homologs: The when and the how. Biophysica 1999:44(6): 980-91.
2000    
[205] PDF
 D. Gront A. Kolinski and J. Skolnick. Comparison of three Monte Carlo conformational search strategies for protein-like polymer models: Identification of low energy structures and folding thermodynamics. J Chem Phys 2000:113(12).
[204] PDF
 M. Feig, P. Rotkiewicz, A. Kolinski, J. Skolnick and C. Brooks. Accurate reconstruction of all-atom protein representations from side chain based low-resolution models. Proteins 2000:41: 86-97.
[203] PDF
 J. Skolnick and D. Kihara. Defrosting the frozen approximation: PROSPECTOR: A new approach to threading. Proteins 2001:42: 319-31.
[202] PDF
 J. Fetrow, N. Siew, M. Yamout, J. Dyson, P. Wright and J. Skolnick. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight. Protein Science 2001:10: 1005-1014.
[201] PDF
 B. Ilkowski, J. Skolnick and A. Kolinski. Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model. Macromolecular Theory and Simulations 2000:9: 523-533.
[200] PDF
 A. Kolinski, P. Rotkiewicz, B. Ilkowski and J. Skolnick. Protein folding: Flexible lattice models. Prog. Theor. Phys. 2000:138: 292-300.
[199] PDF
 J. Skolnick, J. S. Fetrow and A. Kolinski. Structural genomics and its importance for gene function analysis. Nature Biotechnology 2000:18: 283-7.
[198] PDF
 J. Skolnick, A. Kolinski and A. Ortiz. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 2000:38: 3-16.
[197] PDF
 J. Skolnick and J.S. Fetrow. From genes to protein structure and function: Novel applications of computational approaches in the genomic era. TIBTECH 2000:18: 34-9.
1991-1999    
[196] PDF
 A. Kolinski, B. Ilkowski and J. Skolnick. Dynamics and thermodynamics of -hairpin assembly: Insight from various simulation techniques. Biophys J 1999:77: 2942-52.
[195] PDF
 A.R. Ortiz and J. Skolnick. Sequence evolution and the mechanism of protein folding. Biophys J 1999:79: 1787-1799.
[194] PDF
 A. Sikorski, A. Kolinski and J. Skolnick. Computer simulations of the properties of some de novo designed helical proteins. Proteins 2000:38: 17-28.
[193] PDF
 A.R. Ortiz, A. Kolinski, P. Rotkiewicz, B. Ilkowski and J. Skolnick. CASP3 Proceedings: Ab initio folding of proteins using restraints derived from evolutionary information. Proteins Suppl 1999:3: 177-185.
[192] PDF
 J.S. Fetrow, N. Siew and J. Skolnick. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine-threonine protein phosphatase-1 subfamily. FASEB J 1999:13: 1866-1874.
[191] PDF
 B. Zhang, L. Rychlewski, K. Pawlowski, J. Fetrow, J. Skolnick and A. Godzik. From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions. Protein Science 1999:8: 1104-1115.
[190]
J. Skolnick, J. Fetrow, A.R. Ortiz and A. Kolinski. The role of computational biology in the genomics revolution. Proceedings of the National Research Council's Chemical Sciences Roundtable Workshop on the Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology.
[189] PDF
 C. Keasar, D. Tobi, R. Elber and J. Skolnick. Coupling the folding of homologous proteins. Proc Natl Acad Sci USA 1998:95: 5880-5883.
[188] PDF
 D. Mohanty, B. Dominy, A. Kolinski, C.L. Brooks III and J. Skolnick. Correlation between knowledge-based and detailed atomic potentials for GCN4-lz unfolding. Proteins 1999:35: 447-452.
[187] PDF
 A. Kolinski, P. Rotkiewicz, B. Ilkowski and J. Skolnick. A method for the improvement of threading-based protein models. Proteins 1999:37: 593-610.
[186] PDF
 D.C. Rapaport, J.E. Johnson and J. Skolnick. Supramolecular self-assembly: Molecular dynamics modeling of polyhedral shell formation. Computer Physics Commun 1998.
[185] PDF
 D. Mohanty, A. Kolinski and J. Skolnick. De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. Biophysical J 1999:77: 54-69.
[184] PDF
 L. Zhang, A. Godzik, J. Skolnick and J. Fetrow. Functional analysis of Escherichia coli proteins for members of the hydrolase family. Folding & Design 1998:3: 535-548.
[183] PDF
 J. Skolnick, A. Kolinski and D. Mohanty. De novo predictions of the quaternary structure of leucine zippers and other coiled coils. Int'l J Quantum Chem 1999:75: 165-176.
[182]
J. Skolnick, A. Kolinski and A. Ortiz. Reduced protein models and their application to the protein folding problem. J Biomolec Structure & Dynamics 1998:16: 381-396.
[181] PDF
 B. Reva, J. Skolnick and A.V. Finkelstein. Averaging interaction energies over homologs improves protein fold recognition in gapless threading. Proteins 1999:35: 353-359.
[180] PDF
 C. Simmerling, M. Lee, A.R. Ortiz, A. Kolinski, J. Skolnick and P.A. Kollman. Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: application to the small protein CMTI-1. J Amer Chem Soc 2000:122(35): 8392-8402.
[179] PDF
 K. Witte, J. Skolnick and C-H. Wong. A synthetic retrotransition (backwards reading) sequence of the right handed three-helix bundle domain B (10-53) of protein A shows similarity in conformation as predicted by computation. J Amer Chem Soc 1999:120: 13042-13045.
[178]
A. Kolinski, A. Godzik and J. Skolnick. Contact maps. In: Creighton, T.E., ed. The Encyclopedia of Molecular Biology. New York: John Wiley & Sons, 1999: 567-71.
[177]
J. Skolnick, A. Kolinski and A. Ortiz. Computational molecular biology for the series theoretical and computational chemistry. In: Leszczynski, J., ed. Application of reduced models to protein structure prediction. Amsterdam: Elsevier, 1999: 397-440.
[176]
B. Reva, A.V. Finkelstein and J. Skolnick. Optimization of protein structure on lattices using a self-consistent field approach. J Comput Biol 1998:5: 531-538.
[175]
A. Kolinski, P. Rotkiewicz and J. Skolnick. Application of a high coordination lattice model in protein structure prediction. Proceedings of the Workshop on Monte Carlo Approach to Biopolymers and Protein Folding. Singapore: World Scientific, 1998: 377-388.
[174]
B. Reva, A. Finkelstein and J. Skolnick. A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB98) and J Comput Biol Special Issue, 1998.
[173]
B. Reva, A. Finkelstein and J. Skolnick. Derivation and testing residue-residue mean force potentials for use in protein structure recognition. In: Webster, D. M. ed. Protein Structure Prediction Methods and Protocols. Methods in Molecular Biology series. Bath, U.K.: Humana Press, 1999.
[172] PDF
 J. Fetrow, A. Godzik and J. 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. J Mol Biol 1998:282: 703-711.
[171]
B. Reva, A.V. Finkelstein and J. Skolnick. What is the probability of a chance prediction of a protein structure with an RMSD of 6 Å? Folding & Design 1998:3: 141-147.
[170] PDF
 J. S. Fetrow and J. 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. J Mol Biol 1998:281: 949-968.
[169] PDF
 L. Zhang and J. Skolnick. What should the Z-score of native protein structures be? Protein Sci 1998:7: 1201-1207.
[168] PDF
 A. Ortiz, A. Kolinski and J. Skolnick. Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. Proc Natl Acad Sci USA 1998:95: 1020-1025.
[167]
A. Kolinski, L. Jaroszewski, P. Rotkiewicz and J. Skolnick. An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass. J Chem Phys 1998:102: 4628-4637.
[166] PDF
 M. Milik, D. Sauer, A. Brunmark, M. Jackson, P. Peterson, J. Skolnick and C. Glass. Application of an artificial neural network to predict specific Class I MHC binding peptide sequences. Nature Biotech 1998:16: 753-56.
[165] PDF
 A. Kolinski, W.Galazka and J.Skolnick. Monte Carlo studies of the thermodynamics and kinetics of reduced protein models. Application to small helical, / and proteins. J Chem Physics 1998:108: 2608-2617.
[164]
A. Ortiz, A. Kolinski and J. Skolnick. Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins. Proceedings of the Pacific Symposium on Biocomputing (PSB-98). Altman, R., A.K. Dunker, L. Hunter and T.E. Klein, eds. Singapore: World Scientific Pub. 1998: 377-388.
[163] PDF
 A. Kolinski and J. Skolnick. Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model. Proteins 1998:32: 475-494.
[162] PDF
 A. Ortiz, A. Kolinski and J. 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: 287-294.
[161]
A. Ortiz, W-P. Hu, A. Kolinski and J. Skolnick. Method for low resolution prediction of small protein tertiary structure. Proceedings of the Pacific Symposium on Biocomputing 1997. R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, eds. Singapore: World Scientific Pub., 1997: 316-327.
[160] PDF
 L. Zhang and J. Skolnick. How do potentials derived from structural databases relate to "true" potentials? Protein Sci 1998:7: 112-122.
[159]
J.Skolnick and A. Kolinski. Monte Carlo approaches to the protein folding problem. In: Ferguson, D., J.I. Siepmann, D.G.Truhlar, eds. Monte Carlo Methods in Chemical Physics. Advances in Chemical Physics Series. John Wiley & Sons, 1998: 203-242.
[158] PDF
 B. Reva, A. Finkelstein, M. Sanner, A. Olson and J. Skolnick. Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein Eng 1997:10: 1123-1130.
[157] PDF
 W-P. Hu, A. Kolinski and J. Skolnick. Improved method for the prediction of the protein backbone U-turn positions and the major secondary structures between the U-turns. Proteins 1997:29: 443-460.
[156] PDF
 A. Ortiz, A. Kolinski and J. Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 1998:277: 419-448.
[155] PDF
 A.Sikorski, A. Kolinski and J. Skolnick. Computer simulations of de novo designed helical proteins. Biophys J 1998:75: 92-105.
[154] PDF
 C. Keasar, R. Elber and J. Skolnick. Simultaneous and coupled energy optimization of homologous proteins: A new tool for structure prediction. Folding & Design 1997:2: 247-259.
[153] PDF
 A. Kolinski and J. Skolnick. Determinants of secondary structure of polypeptide chains: interplay between short range and burial interactions. J Chem Physics 1997:107: 953-964.
[152] PDF
 J. Skolnick, L. Jaroszewski, A. Kolinski and A. Godzik. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997:6: 676-688.
[151]
J. Skolnick. A Monte Carlo model of fd and Pf1 coat proteins in membranes. Chemtracts 1997:10: 242-245.
[150]
A. Kolinski and J. Skolnick. High coordination lattice models of protein structure, dynamics and thermodynamics. Acta Biochimica Polonica (Review) 1997:44: 389-422.
[149] PDF
 W-P.Hu, A. Godzik and J. Skolnick. Sequence-structure specificity-how does an inverse folding approach work? Protein Eng 1997:10: 317-331.
[148] PDF
 A. Kolinski, J. Skolnick, A. Godzik and W-P Hu. A method for the prediction of surface "U"-turns and transglobular connections in small proteins. Proteins 1997:27: 290-308.
[147] PDF
 J. Skolnick, A. Kolinski and A. Ortiz. MONSSTER: A method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997:265: 217-241.
[146]
J. Skolnick and M. Milik. Modeling of Membrane Proteins and Peptides. In: von Heijne, G., ed. Membrane Proteins Assembly, Part IV. Modeling and Simulation, Austin: R.G. Landes Company, 1997:201-220.
[145] PDF
 M. Milik, A. Kolinski and J. Skolnick. Algorithm for rapid reconstruction of a protein backbone from alpha carbon coordinates. J Comput Chem 1997:18: 80-85.
[144]
J. Skolnick and A. Kolinski. Protein Modeling. In: Schleyer, P. and P. Kollman, eds. Encyclopedia of Computational Chemistry. Sussex, England: John Wiley & Sons, 1998: 2200-2211.
[143]
J. Skolnick and A. Kolinski. Monte Carlo Lattice Dynamics and the Prediction of Protein Folds. Computer Simulations of Biomolecular Systems. In: van Gunsteren, W. F., P.K. Weiner and A. J. Wilkinson, eds. Theoretical and Experimental Studies. Leiden, The Netherlands: ESCOM Science, 1997: 395-429.
[142]
M. Vieth, A. Kolinski, C. Brooks, III and J. Skolnick. Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants. Proc. Pacific Symposium on Biocomputing (PSB-96). Hunter, L., T. Klein, eds. World Scientific, Singapore, 1996: 653-662 (1996).
[141]
A. Kolinski, J. Skolnick and A. Godzik. An algorithm for prediction of structural elements in small proteins. Proc. Pacific Symposium on Biocomputing (PSB-96). Hunter, L., T. Klein, eds. World Scientific, Singapore, 1996: 446-460.
[140] PDF
 J. Hirst, M. Vieth, J. Skolnick and C. L. Brooks III. Predicting leucine zipper structures from sequence. Protein Eng 1996:9: 657-662.
[139]
A. Kolinski and J. Skolnick. Lattice Models of Protein Folding, Dynamics and Thermodynamics. Austin: R.G. Landes Company, 1996: 202.
[138] PDF
 A. Kolinski, W. Galazka and J. Skolnick. On the origin of the cooperativity of protein folding: Implications from model simulations. Proteins 1996:26: 271-287.
[137] PDF
 K. Olszewski, A. Kolinski and J. Skolnick. Does a backwardly read protein sequence have a unique native state? Protein Eng 1996:9: 5-14.
[136] PDF
 S. DeBolt and J. 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 Eng 1996:9: 637-655.
[135] PDF
 M. Vieth, A. Kolinski and J. Skolnick. Method for predicting the state of association of discretized protein models. Application to leucine zippers. Biochemistry 1996:35: 955-967.
[134]
M. Vieth, A. Kolinski, C. L. Brooks III, and J. Skolnick. A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants. DIMACS 1996:23: 233-236.
[133] PDF
 K. Olszewski, A. Kolinski and J. Skolnick. Folding simulations and computer redesign of protein A three-helix bundle motifs. Proteins 1996:25: 286-299.
[132]
J. Skolnick and M. Milik. Monte Carlo Models of Spontaneous Insertion of Peptides into Lipid Membranes. In: Merz, K., B. Roux, eds. Membrane Structures & Dynamics. Boston: Birkhauser, 1996: 535-554.
[131] PDF
 A. Godzik, A. Kolinski and J. Skolnick. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci 1995:4: 2107-2117.
[130]
M. Milik and J. Skolnick. A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. Biophys J 1995:69: 1382-1386.
[129] PDF
 A. Baumgäner and J. Skolnick. Polymer electrophoresis across a model membrane. J Phys Chem 1995:98: 10655-10658.
[128] PDF
 A. Kolinski, W. Galazka and J. Skolnick. Computer design of idealized β-motifs. J Chem Phys 1995:103: 10286-10297.
[127] PDF
 A. Kolinski, M. Milik, J. Rycombel and J. Skolnick. A reduced model of short range interactions in polypeptide chains. J Chem Phys 1995:103: 4312-4323.
[126] PDF
 A. Baumgäner and J. Skolnick. Spontaneous translocation of a polymer across a curved membrane. Phys Rev Letters 1995:74: 2142-2145.
[125]
M. Milik and J. Skolnick. An object oriented environment for artificial evolution of protein sequences: The example of rational design of transmembrane sequences. Evolutionary Conference (1995).
[124]
J. Skolnick, M. Vieth, A. Kolinski and C. Brooks III. De novo simulations of the folding of GCN4 and its mutants. In: A. Pullman, et al., eds. Modeling of Biomolecular Structures and Mechanisms. Kluwer Acad./Netherlands 1995:8: 95-98.
[123] PDF
 M. Vieth, A. Kolinski, C. L. Brooks III and J. Skolnick. Prediction of the quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. J Mol Biol 1995:251: 448-467.
[122] PDF
 M. Vieth, A. Kolinski and J. Skolnick. A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations. J Chem Phys 1995:102: 6189-6193.
[121]
M. Milik, A. Kolinski and J. Skolnick. Neural network system for the evaluation of side-chain packing in protein structures. Protein Eng 1995:8: 225-236.
[120] PDF
 A. Sikorski, A. Kolinski and J. Skolnick. Dynamics of star branched polymers in a matrix of linear chains. A Monte Carlo study. Macromolecular Theory and Simulations 1994:3: 715-719.
[119]
J. Skolnick and A. Kolinski. De novo prediction of protein tertiary structure. Polymer Preprints 1994:35: 82-83.
[118]
A. Godzik and J. Skolnick. Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS 1994:10: 587-596.
[117]
A. Kolinski and J. Skolnick. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins 1994:18: 353-366.
[116]
A. Kolinski and J. Skolnick. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 1994:18: 338-352.
[115] PDF
 A. Rey and J. Skolnick. Computer simulation of the folding of coiled coils. J Chem Phys 1994:100: 2267-2276.
[114] PDF
 M. Vieth, A. Kolinski, C. L. Brooks, III and J. Skolnick. Prediction of the folding pathways and structure of the GCN4 "leucine zipper." J Mol Biol 1994:237: 361-367.
[113]
A. Godzik, A. Kolinski and J. Skolnick. Lattice representation of globular proteins: How good are they? J Comput Chem 1994:14: 1194-1202.
[112]
A. Godzik, J. Skolnick and A. Kolinski. Regularities in interaction patterns of globular proteins. Protein Eng 1993:6: 801-810.
[111]
J. Skolnick, A. Kolinski, C. L. Brooks, III, A. Godzik and A. Rey. A method for prediction of protein structure from sequence. Current Biology 1993:3: 414-423.
[110]
A. Godzik, A. Kolinski and J. Skolnick. De novo and inverse folding predictions of protein structure and dynamics. J Comput-Aided Mol Design 1993:7: 397-438.
[109]
M. Baginski, L. Piela and J. Skolnick. The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis. J Comput Chem 1993:14: 471-477.
[108] PDF
 J. Skolnick, A. Kolinski and A. Godzik. From independent modules to molten globules: Observations on the nature of protein folding intermediates. Commentary in Proc Natl Acad Sci USA 1993:90: 2099-2100.
[107] PDF
 A. Kolinski, A. Godzik and J. Skolnick. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins. Application to designed helical proteins. J Chem Phys 1993:98: 7420-7433.
[106] PDF
 Y. Levine, A. Kolinski and J. Skolnick. A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids. J Chem Phys 1993:98: 7581-7587.
[105] PDF
 A. Kolinski and J. Skolnick. Comment on local knot model of entangled polymer chains. J Phys Chem 1993:97: 3450.
[104] PDF
 M. Milik and J. Skolnick. Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model. Proteins 1993:15: 10-25.
[103] PDF
 A. Rey and J. Skolnick. Computer modeling and folding of four-helix bundles. Proteins 1993:16: 8-28.
[102] PDF
 K. L. Ngai, S. L. Peng and J. Skolnick. Generalized Fokker-Planck approach to the coupling model and comparison with computer simulation. Macromolecules 1992:25: 2184-2191.
[101] PDF
 A. Godzik and J. Skolnick. Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA 1992:89: 12098-12102.
[100] PDF
 A. Kolinski and J. Skolnick. Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides. J Chem Phys 1992:98: 9412-9426.
[99]
M. Vieth, A. Kolinski, J. Skolnick and 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: 369-392.
[98] PDF
 A. Rey, A. Kolinski, J. Skolnick and Y. Levine. Effect of double bonds on the dynamics of hydrocarbon chains. J Chem Phys 1992:97: 1240-1249.
[97] PDF
 M. Milik and J. Skolnick. Spontaneous insertion of polypeptide chains into membranes: A Monte Carlo model. Proc Natl Acad Sci USA 1992:89: 9391-9395.
[96]
A. Godzik, J. Skolnick and A. Kolinski. A topology fingerprint approach to the inverse protein folding problem. J Mol Biol 1992:227: 227-238.
[95] PDF
 M. Milik, J. Skolnick and A. Kolinski. Monte Carlo studies of an idealized model of a lipid-water system. J Phys Chem 1992: 96: 4015-4022.
[94]
A. Rey and J. Skolnick. Efficient algorithm for the reconstruction of a protein backbone from the -carbon coordinates. J Comput Chem 1992:13: 443-456.
[93] PDF
 A. Godzik, J. Skolnick and A. Kolinski. Simulations of the folding pathway of triose phosphate isomerase-type / barrel proteins. Proc Natl Acad Sci USA 1992:89: 2629-2633.
[92] PDF
 A. Rey and J. Skolnick. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of -helical hairpins. Chemical Physics 1991:158: 199-219.
[91] PDF
 Y. Levine, A. Kolinski and J. Skolnick. Monte Carlo dynamics study of motions in CIS-unsaturated hydrocarbon chains. J Chem Phys 1991:95: 3826-3834.
[90]
J. Skolnick and A. Kolinski. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure, and dynamics. J Mol Biol 1991:221: 499-531.
[89] PDF
 A. Kolinski, M. Milik and J. Skolnick. Static and dynamic properties of a new lattice model of polypeptide chains. J Chem Phys 1991:94: 3978-3985.
[88] PDF
 K. L. Ngai and J. Skolnick. Correspondence between coupling theory and computer simulations. The diffusion of a probe polymer in a matrix having different degrees of polymerization. Macromolecules 1991: 24: 1561-1566.
1977-1990    
[87] PDF
 J. Skolnick and A. Kolinski. Simulations of the folding of a globular protein. Science 1990:250: 1121-1125.
[86] PDF
 M. Milik, A. Kolinski and J. Skolnick. Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model. J. Chem. Phys 1990:93: 4440-4446.
[85]
J. Skolnick, A. Kolinski and A. Sikorski. Dynamic Monte Carlo simulations of globular protein and structure. Chemical Design Automation News 1990:5: 1-20.
[84]
J. Skolnick, A. Kolinski and A. Sikorski. Dynamic Monte Carlo simulations of globular protein folding, structure and dynamics. Comments on Mol. & Cell. Biol 1990:6: 223-247.
[83]
A. Sikorski and J. Skolnick. Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member β-barrels. J Mol Biol 1990:215: 183-198.
[82]
A. Sikorski and J. Skolnick. Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. -helical motifs. J Mol Biol 1990:212: 819-836.
[81]
J. Skolnick and A. Kolinski. Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six member, Greek key -barrels. J Mol Biol 1990:212: 787-817.
[80]
J. Skolnick and A. Kolinski. Dynamics of dense polymer systems: Computer simulations and analytic theories. Advances in Chemical Physics 1990:77: 223-278.
[79]
A. Holtzer, M.E. Holtzer and J. Skolnick. Does the unfolding transition of two-chain, coiled coil proteins involve a continuum of intermediates? AAAS Seminar Volume on The Protein Folding Problem (1990).
[78]
J. Skolnick and A. Kolinski. Computer simulations of globular protein folding and tertiary structure. Annu Rev Phys Chem 1989:40: 207-235.
[77]
J. Skolnick. Dynamics of dense polymer systems. Dynamic Monte Carlo simulation results and analytic theory. In: Dorfmuller, T., ed. Reactive and Flexible Molecules Liquids. Klumer Academic Publishers, 1989:291: 199-220.
[76]
J. Skolnick, A. Kolinski, A. Sikorski and R. Yaris. Dynamic Monte Carlo simulation of a melt of ring polymers. Polymer Preprints 1989:30: 70-73.
[75] PDF
 A. Sikorski and J. Skolnick. Monte Carlo simulation of equilibrium globular protein folding: -helical bundles with long loops. Proc Natl Acad Sci USA 1989:86: 2668-2672.
[74] PDF
 J. Skolnick, A. Kolinski and R. Yaris. Dynamic Monte Carlo study of the folding of a six stranded Greek key globular protein. Proc Natl Acad Sci 1989:86: 1229-1233.
[73] PDF
 A. Sikorski and J. Skolnick. Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle. Biopolymers 1989:28: 1097-1113.
[72]
J. Skolnick, A. Kolinski and R. Yaris. Monte Carlo studies on equilibrium globular protein folding. II. -barrel globular protein models. Biopolymers 1989:28: 1059-1095.
[71]
A. T. Yeates, J. Skolnick and R. Yaris. Fit of a nonreptative model of polymer melt dynamics to experimental melt diffusion constant measurements. J Poly Sci Poly Phys Ed 1989:27: 151-154 (1989).
[70]
J. Skolnick, R. Yaris, and A. Kolinski. Phenomenological theory of polymer melt dynamics. Int J Mod Phys 1989:3: 33-64.
[69] PDF
 J. Skolnick, A. Kolinski and R. Yaris. Monte Carlo simulations of the folding of β-barrel globular proteins. Proc Natl Acad Sci USA 1988:85: 5057-5061.
[68] PDF
 A. J. Barrett and J. Skolnick. On the apparent radius of gyration of linear polymers and the experimental determination of the excluded volume parameter. Macromolecules 1988:21: 1141-1145.
[67] PDF
 J. Skolnick and R. Yaris. Phenomenological theory of the dynamics of polymer melts. II. Viscoelastic properties. J Chem Phys 1988:88: 1418-1442.
[66] PDF
 J. Skolnick, R. Yaris and A. Kolinski. Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion. J Chem Phys 1988:88: 1407-1417.
[65]
A. Holtzer and J. Skolnick. Application of the augmented theory of -helix-to-random-coil transitions of two-chain, coiled coils to extant data on synthetic, tropomyosin-analog peptides. Biopolymers 1988:27: 87-96.
[64] PDF
 J. Skolnick, A. Kolinski and R. Yaris. Monte Carlo studies of the long time dynamics of dense polymer systems. The failure of the reptation model. Accts Chem Research 1987:20: 350-356.
[63]
A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of -barrel proteins. Biopolymers 1987:26: 937-962.
[62] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization. J Chem Phys 1987:86: 7174-7180.
[61] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt. J Chem Phys 1987:86: 7164-7173.
[60] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Does reptation describe the dynamics of entangled finite length polymer systems? A model simulation. J Chem Phys 1987:86: 1567-1585.
[59]
J. Skolnick. Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction. Biophys J 1987:51: 227-243.
[58] PDF
 D. Perchak, J. Skolnick and R. Yaris. Computer simulations of simple models of the ring-flip process in polycarbonate. Macromolecules 1987:20: 121-129.
[57] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Dynamic Monte Carlo study of the conformational properties of long flexible polymers. Macromolecules 1987:20: 438-440.
[56]
J. Skolnick. Theory of the helix-coil transition in doubly cross-linked, two-chain, coiled coils. A globular protein model. In: Eisenfeld, J. and M. Witten, eds. Modeling of Biomedical Systems. 1986: 167-172.
[55]
P. Duffy, J. Skolnick and A. Holtzer. A theoretical model simulating the anomalous concentration dependence of the equilibrium thermal unfolding curve of non-cross-linked tropomyosin. Biochem Biophys Res Commun 1986:141: 394-398.
[54] PDF
 A. Kolinski, J. Skolnick and R. Yaris. The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system. J Chem Phys 1986:85: 3585-3597.
[53] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo simulations on an equilibrium globular protein folding model. Proc Natl Acad Sci USA 1986:83: 7267-7271.
[52] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Order-disorder transitions in tetrahedral lattice polymer systems. Macromolecules 1986:19: 2560-2567.
[51] PDF
 A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo study of local orientational order in a semiflexible polymer melt model. Macromolecules 1986:19: 2550-2560.
[50] PDF
 A. Holtzer and J. Skolnick. Theory of -helix to random coil transition of two-chain, coiled coils. Application of the augmented theory to thermal denaturation of -tropomyosin. Macromolecules 1986:19: 1769-1770.
[49] PDF
 J. Skolnick and A. Holtzer. -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: 6192-6202.
[48] PDF
 J. Skolnick. Theory of the helix-coil transition in doubly cross-linked, two-chain, coiled coils. A globular protein model. Macromolecules 1986:19: 1153-1166.
[47] PDF
 A. Kolinski, J. Skolnick and R. Yaris. On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system. J Chem Phys 1986:84: 1922-1931.
[46] PDF
 C. L. Chen and J. Skolnick. Theory of the helix-coil transition in singly cross-linked, two-chain, coiled coils. II. Role of mismatched states. Macromolecules 1986:19: 242-243.
[45]
A. Kolinski, J. Skolnick and R. Yaris. Monte Carlo dynamics of diamond-lattice multichain systems. Proceedings of the 1985 La Jolla Workshop on Polymer Flow Interaction. AIP Conference Proceedings, (Y. Rabin, ed.) 1985:137: 241-245.
[44]
J. Skolnick. Role of topological constraints in the all-or-none transition of a globular protein model. Theory of the helix-coil transition in doubly cross-linked, coiled coils. Biochem Biophys Res Commun 1985:129: 848-853.
[43]
J. Skolnick. Theory of the helix-coil transition in two-chain, coiled coils. A globular protein folding model. 11th IMACS World Congress Proceedings 1985:2: 259.
[42] PDF
 J. Skolnick and A. Holtzer. Theory of -helix-to-random coil transition of two-chain, coiled coils. Application of the augmented theory to thermal denaturation of tropomyosin. Macromolecules 1985:18: 1549-1559.
[41] PDF
 J. Skolnick. Theory of the helix-coil transition in singly cross-linked, two-chain, coiled coils. Macromolecules 1985:18: 1535-1549.
[40] PDF
 J. Skolnick and R. Yaris. Damped orientational diffusion model of polymer local main chain motion. 5. Comparison with three alternative models. Macromolecules 1985:18: 1635-1637.
[39] PDF
 J. Skolnick. Theory of helix-coil transition in single chain polypeptides with interhelical contacts. The broken -helical hairpin model. Macromolecules 1985:18: 1073-1083.
[38] PDF
 D. Perchak, J. Skolnick and R. Yaris. Dynamics of rigid and flexible constraints for polymers. Effect of the Fixman potential. Macromolecules 1985:18: 519-525.
[37] PDF
 J. Schaefer, E.O. Stejskal, D. Perchak, J. Skolnick and R. Yaris. Molecular mechanism of the ring-flip process in polycarbonate. Macromolecules 1985:18: 368-373.
[36] PDF
 B. Pant, J. Skolnick and R. Yaris. Damped orientational diffusion model of polymer local main chain motion. 4. Effects of probes and side chains. Macromolecules 1985:18: 253-259.
[35] PDF
 J. Skolnick. Theory of the kinetics of the helix-coil transition in two-chain, coiled coils. 2. The finite chain. Macromolecules 1985:18: 232-243.
[34] PDF
 J. Skolnick, D. Perchak, R. Yaris and J. Schaefer. Phenomenological model of the stress-strain behavior of glassy polymers. Macromolecules 1984:17: 2332-2336.
[33] PDF
 J. Skolnick. Theory of the kinetics of the helix-coil transition in two-chain, coiled coils. 1. Infinite chain limit. Macromolecules 1984:17: 2158-2173.
[32] PDF
 J. Skolnick. Theory of helix-coil transitions of -helical, two-chain, coiled coils. Analytic treatment of the homopolymeric, neglect-loop-entropy model. Macromolecules 1984:17: 2153-2158.
[31] PDF
 J. Skolnick, D. Perchak and R. Yaris. Restricted internal segmental rotational diffusion model with segment-segment interactions. Application to 13C NMR. J Mag Reson 1984:57: 204-220.
[30] PDF
 J. Skolnick. Effect of loop entropy on the helix-coil transition of -helical, two-chain, coiled coils. 3. Supermatrix formulation of the imperfect-matching model. Macromolecules 1984:17: 645-658.
[29] PDF
 J. Skolnick. Effect of loop entropy on the helix-coil transition of -helical, two-chain, coiled coils. 2. Supermatrix formulation of the perfect-matching model. Macromolecules 1983:16: 1763-1770.
[28] PDF
 J. Skolnick and A. Holtzer. Theory of -helix-to-random-coil transitions of two-chain coiled coils. Application to the T1 and T2 fragments of -tropomyosin. Macromolecules 1983:16: 1548-1550.
[27] PDF
 D. Perchak, R. Yaris and J. Skolnick. Effects of topological solitons on autocorrelation functions for chains of coupled torsional oscillators. J Chem Phys 1983:78: 6914-6927.
[26] PDF
 J. Skolnick. Effect of loop entropy on the helix-coil transition of -helical, two-chain, coiled coils. Macromolecules 1983:16: 1069-1083.
[25] PDF
 M. E. Holtzer, A. Holtzer and J. Skolnick. -Helix to random coil transition of two-chain, coiled coils. Theory and experiments for thermal denaturation of -tropomyosin at acidic pH. Macromolecules 1983:16: 462-465.
[24] PDF
 J. Skolnick and R. Yaris. Damped orientational diffusion model of polymer local main-chain motion. 3. Inclusion of chain-chain interactions. Macromolecules 1983:16: 266-272.
[23] PDF
 M. E. Holtzer, A. Holtzer and J. Skolnick. -helix-to-random-coil transition of two-chain, coiled coils. Theory and experiments for thermal denaturation of -tropomyosin. Macromolecules 1983:16: 173-180.
[22]
J. Skolnick. An order-disorder theory of stress-strain behavior of glassy polymers In: Pethrick, A. and R.W. Richards, eds. Static and Dynamic Properties of the Polymeric Solid State. Boston: D. Reidel Publishing Company, 1982.
[21] PDF
 E. Helfand and J. Skolnick. Mechanism and rates of conformational transitions in heterogeneous polymers. J Chem Phys 1982:77: 5714-5724.
[20] PDF
 J. Skolnick and R. Yaris. Damped orientational diffusion model of polymer local main-chain motion. 2. Application to poly (vinyl acetate). Macromolecules 1982:15: 1046-1051.
[19] PDF
 J. Skolnick and R. Yaris. Damped orientational diffusion model of polymer local main chain polymer motion. 1. General theory. Macromolecules 1982:15: 1041-1046.
[18] PDF
 W. L. Mattice and J. Skolnick. Stability of the cross-linked tropomyosin dimer: Cross-link effect on the cooperativity of the ordering process and on the maximum in the helix probability profile. Macromolecules 1982:15: 1088-1093.
[17] PDF
 J. Skolnick and A. Holtzer. Theory of -helix-to-random coil transitions of two-chain, coiled coils. Application to a synthetic analogue of tropomyosin. Macromolecules 1982:15: 812-821.
[16] PDF
 J. Skolnick and A. Holtzer. Theory of helix-coil transitions of -helical, two-chain, coiled coils. Macromolecules 1982:15: 303-314.
[15] PDF
 E. Helfand, Z. Wasserman, T. Weber, J. Skolnick and J.H. Runnels. The kinetics bonds of conformational transitions: Effects of variation of bond angle bending and bond stretching force constants. J Chem Phys 1981:75: 4441.
[14] PDF
 W. L. Mattice and J. Skolnick. Trans placements, expansion and asymometry of star like polyethylenes bearing similarly charged ends. Macromolecules 1981:14: 1463-1468.
[13] PDF
 D. K. Carpenter and J. Skolnick. Depolarized light scattering from macromlecules: Effects of torsional oscillations, conformational transitions and overall rotations. Macromolecules. 1981:14: 1284-1290.
[12] PDF
 W. L. Mattice and J. Skolnick. Conformational properties of bolaform electrolytes. Macromolecules. 1981: 14: 863-867.
[11] PDF
 J. Skolnick. Kinetics of conformational transitions in polymers containing skeletal double bonds. Macromolecules 1981:14: 646-654.
[10] PDF
 J. Skolnick and W.L. Mattice. Rates of conformational transitions in branched chain molecules. Macromolecules. 1981:14: 292-299.
[9] PDF
 J. Skolnick and A.M. Holtzer. Effect of urea on the intrinsic viscosity of randomly coiled poly (a-L-glutamate). Macromolecules 1980:13: 1311-1313.
[8] PDF
 J. Skolnick and E. Helfand. Kinetics of conformational transitions in chain molecules. J Chem Phys 1980:72: 5489-5500.
[7] PDF
 J. Skolnick and E.K. Grimmelman. A preliminary examination of end effects in polyelectrolyte theory: The potential of a line segment of charge. Macromolecules 1980:13: 335-338.
[6] PDF
 J. Skolnick. Colligative properties of helical polyelectrolytes. Macromolecules 1979:12: 515-521.
[5]
J. Skolnick and M. Fixman. Screened coulomb interactions on a dielectric cylinder. Polym Preprints 1978:19: 247.
[4] PDF
 J. Skolnick and M. Fixman. Charge interactions in cylindrical polyelectrolytes. Macromolecules. 1978:11: 867.
[3] PDF
 M. Fixman and J. Skolnick. Polyelectrolyte excluded volume paradox. Macromolecules 1978:11: 863-867.
[2]
J. Skolnick. Investigations on a rod-like polyelectrolyte model. Ph.D. Thesis. Yale University (1978).
[1] PDF
 J. Skolnick and M. Fixman. Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 1977:10: 944-948.