2006
Szilágyi, A, Skolnick J. 2006. Efficient prediction of nucleic acid binding function from low-resolution protein structures. Journal of molecular biology. 358(3):922-33. PDF
Grimm, V, Zhang Y, Skolnick J. 2006. Benchmarking of dimeric threading and structure refinement. Proteins. 63(3):457-65. PDF
Lee, S Y, Zhang Y, Skolnick J. 2006. TASSER-based refinement of NMR structures. Proteins. 63(3):451-6. PDF
Zhang, Y, Hubner IA, Arakaki AK, Shakhnovich EI, Skolnick J. 2006. 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. 103(8):2605-10. PDF Supplementary Data
Zhang, Y, Devries ME, Skolnick J. 2006. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS computational biology. 2(2):e13. PDF Supplementary Data
Pandit, S B, Zhang Y, Skolnick J. 2006. TASSER-Lite: an automated tool for protein comparative modeling. Biophysical journal. 91(11):4180-90. PDF
Skolnick, J. 2006. In quest of an empirical potential for protein structure prediction. Current opinion in structural biology. 16(2):166-71. PDF
Arakaki, AK, Tian W, Skolnick J. 2006. High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC genomics. 7:315. PDF
2005
Bindewald, E, Skolnick J. 2005. A scoring function for docking ligands to low-resolution protein structures. Journal of computational chemistry. 26(4):374-83. PDF
Szilágyi, A, Grimm V, Arakaki AK, Skolnick J. 2005. Prediction of physical protein-protein interactions. Physical biology. 2(2):S1-16. PDF
Zhang, Y, Skolnick J. 2005. 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. 102(4):1029-34. PDF
Skolnick, J. 2005. Putting the pathway back into protein folding. Proceedings of the National Academy of Sciences of the United States of America. 102(7):2265-6. PDF
Zhang, Y, Arakaki AK, Skolnick J. 2005. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 61 Suppl 7:91-8. PDF
Zhang, Y, Skolnick J. 2005. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research. 33(7):2302-9. PDF
Skolnick, J, Zhang Y, Kolinski A. 2005. Ab Initio modeling. In: A. Edwards, M. Norin and M. Sundstrom, Eds. Structural Genomics and High Throughput Structural Biology. CRC/Taylor & Francis, Boca Raton, FL, Chapter VIII,137-162.
2004
Betancourt, MR, Skolnick J. 2004. Local propensities and statistical potentials of backbone dihedral angles in proteins. Journal of molecular biology. 342(2):635-49. PDF
Zhang, Y, Skolnick J. 2004. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophysical journal. 87(4):2647-55. PDF
Zhang, Y, Skolnick J. 2004. Automated structure prediction of weakly homologous proteins on a genomic scale. Proceedings of the National Academy of Sciences of the United States of America. 101(20):7594-9. PDF Supplementary Data
Arakaki, AK, Zhang Y, Skolnick J. 2004. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (Oxford, England). 20(7):1087-96. PDF Supplementary Data
Kihara, D, Skolnick J. 2004. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins. 55(2):464-73. PDF
Zhang, Y, Skolnick J. 2004. Scoring function for automated assessment of protein structure template quality. Proteins. 57(4):702-10. PDF
Skolnick, J, Kihara D, Zhang Y. 2004. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins. 56(3):502-18. PDF
Li, W, Zhang Y, Skolnick J. 2004. Application of sparse NMR restraints to large-scale protein structure prediction. Biophysical journal. 87(2):1241-8. PDF
Tian, W, Arakaki AK, Skolnick J. 2004. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic acids research. 32(21):6226-39. PDF
Kolinski, A, Skolnick J. 2004. Reduced models of proteins and their applications. Polymer. 45(2):511-524. PDF
2003
Skolnick, J. 2003. What practical use is protein structure prediction to drug discovery? BioIT World. PDF
Tian, W, Skolnick J. 2003. How well is enzyme function conserved as a function of pairwise sequence identity? Journal of molecular biology. 333(4):863-82. PDF
Li, W, Zhang Y, Kihara D, Huang Y J, Zheng D, Montelione GT, Kolinski A, Skolnick J. 2003. TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 53(2):290-306. PDF
Boniecki, M, Rotkiewicz P, Skolnick J, Kolinski A. 2003. Protein fragment reconstruction using various modeling techniques. Journal of computer-aided molecular design. 17(11):725-38. PDF
Kolinski, A, Klein P, Romiszowski P, Skolnick J. 2003. Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model. Biophysical journal. 85(5):3271-8. PDF
Lu, H, Lu L, Skolnick J. 2003. Development of unified statistical potentials describing protein-protein interactions. Biophysical journal. 84(3):1895-901. PDF Supplementary Data
Pokarowski, P, Kolinski A, Skolnick J. 2003. 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. 84(3):1518-26. PDF
Lu, L, Arakaki AK, Lu H, Skolnick J. 2003. Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome research. 13(6A):1146-54. PDF
Kolinski, A, Gront D, Pokarowski P, Skolnick J. 2003. A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers. 69(3):399-405. PDF
Kihara, D, Skolnick J. 2003. The PDB is a covering set of small protein structures. Journal of molecular biology. 334(4):793-802.PDF
Lu, H, Skolnick J. 2003. Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers. 70(4):575-84. PDF
Haliloglu, T, Kolinski A, Skolnick J. 2003. Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers. 70(4):548-62. PDF
Zhang, Y, Kolinski A, Skolnick J. 2003. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophysical journal. 85(2):1145-64. PDF
Skolnick, J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilágyi A, Kihara D. 2003. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53 Suppl 6:469-79. PDF
2002
Lu, L, Lu H, Skolnick J. 2002. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins. 49(3):350-64. PDF
Viñals, J, Kolinski A, Skolnick J. 2002. Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. Biophysical journal. 83(5):2801-11. PDF
Wojciechowski, M, Skolnick J. 2002. Docking of small ligands to low-resolution and theoretically predicted receptor structures. Journal of computational chemistry. 23(1):189-97. PDF
Fetrow, JS, Giammona A, Kolinski A, Skolnick J. 2002. The protein folding problem: a biophysical enigma. Current pharmaceutical biotechnology. 3(4):329-47. PDF
Zhang, Y, Kihara D, Skolnick J. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48(2):192-201. PDF
Kihara, D, Zhang Y, Lu H, Kolinski A, Skolnick J. 2002. 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. 99(9):5993-8. PDF
Sikorski, A, Kolinski A, Skolnick J. 2002. Computer simulations of protein folding with a small number of distance restraints. Acta biochimica Polonica. 49(3):683-92. PDF
Skolnick, J, Kolinski A. 2002. A Unified Approach to the Prediction of Protein Structure and Function. Computational Methods for Protein Folding: A Special Volume of Advances in Chemical Physics,Volume 120, Edited by Richard A. Friesner, Series Editor I. Prigogine and Stuart A. Rice. John Wiley & Sons, Inc. 131-192. PDF
2001
Betancourt, MR, Skolnick J. 2001. Universal similarity measure for comparing protein structures. Biopolymers. 59(5):305-9. PDF
Di Gennaro, JA, Siew N, Hoffman BT, ZHANG L, Skolnick J, Neilson LI, Fetrow JS. 2001. Enhanced functional annotation of protein sequences via the use of structural descriptors. Journal of structural biology. 134(2-3):232-45. PDF
Bukhman, YV, Skolnick J. 2001. BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics (Oxford, England). 17(5):468-78. PDF
Fetrow, JS, Siew N, Di Gennaro JA, Martinez-Yamout M, Dyson HJ, Skolnick J. 2001. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Science. 10(5):1005-14. PDF
Skolnick, J, Kihara D. 2001. Defrosting the frozen approximation: PROSPECTOR–a new approach to threading. Proteins. 42(3):319-31. PDF
Kihara, D, Lu H, Kolinski A, Skolnick J. 2001. 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. 98(18):10125-30. PDF
Lu, H, Skolnick J. 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 44(3):223-32. PDF
Kolinski, A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. 2001. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins. 44(2):133-49. PDF
Skolnick, J, Kolinski A, Kihara D, Betancourt MR, Rotkiewicz P, Boniecki M. 2001. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.. Proteins. Suppl 5:149-56. PDF
Zhang, Y, Skolnick J. 2001. Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures. The Journal of Chemical Physics. 115(11):5027. PDF
Betancourt, MR, Skolnick J. 2001. Finding the needle in a haystack: educing native folds from ambiguousab initio protein structure predictions. Journal of Computational Chemistry. 22(3):339-353. PDF
Skolnick, J, Kolinski A. 2001. Computational studies of protein folding. Computing in Science & Engineering. 3:22-31. PDF
Gront, D, Kolinski A, Skolnick J. 2001. A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics. Journal of Computational Physics. 115:1569-1574. PDF