2013
Jo, S, Lee H S, Skolnick J, Im W. 2013. Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Computational Biology. 9(3):e1002946. PDF
Skolnick, J, Zhou H, Gao M. 2013. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current opinion in structural biology. 23(2):191-7. PDF
Zhang, Y, Skolnick J. 2013. Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biology. 11(1):44. PDF
Gao, M, Skolnick J. 2013. A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Computational Biology. 9(10):e1003302. PDF
Ando, T, Skolnick J. 2013. On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation. Biophysical Journal. 104(1):96-105. PDF
Skolnick, J, Gao M. 2013. Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National Academy of Sciences. 110(23):9344-9349. PDF
Gao, M, Skolnick J. 2013. APoc: large-scale identification of similar protein pockets.Bioinformatics. 29(5):597-604. PDF
Zhou, H, Skolnick J. 2013. FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. Journal of Chemical Information and Modeling. 53(1):230-240. PDF
Ando, T, Chow E, Skolnick J. 2013. Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations. Journal of Chemical Physics. 139:121922-1. PDF
Ando, T, Skolnick J. 2013. Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. International Conference of the Quantum Bio-Informatics IV. 30:378-387. PDF
2012
Kumar, N, Skolnick J. 2012. EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics. 28(20):2687-2688. PDF
Ando, T, Chow E, Saad Y, Skolnick J. 2012. Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. The Journal of Chemical Physics. 137:064106. PDF
Hammes, GG, Skolnick J. 2012. Biography of Harold A. Scheraga. The Journal of Physical Chemistry B. 116(23):6572-6572. PDF
Hammes, GG, Skolnick J. 2012. Career Accomplishments of Harold A. Scheraga. The Journal of Physical Chemistry B. 116(23):6569-6571. PDF
Zhou, H, Skolnick J. 2012. FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs. Molecular Pharmaceutics. 9(6):1775-1784. PDF
Skolnick, J, Zhou H, Brylinski M. 2012. Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures. The Journal of Physical Chemistry B. 116(23):6654-6664. PDF
Gao, M, Skolnick J. 2012. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proceedings of the National Academy of Sciences. 109(10):3784-3789. PDF
Zhou, H, Skolnick J. 2012. Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF
2011
Kufareva, I, Rueda M, Katritch V, Stevens R C., Abagyan R, Skolnick J, Zhou H, Roy A. 2011. Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment. Structure. 19(8):1108-1126. PDF
Zhou, H, Skolnick J. 2011. GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal. 101(8):2043-2052. PDF
Gao, M, Skolnick J. 2011. New benchmark metrics for protein-protein docking methods. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF
Skolnick, J, Friesner R. 2011. Editorial overview. Current Opinion in Structural Biology. 21:147-149. PDF
Brylinski, M, Skolnick J. 2011. FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins: Structure, Function, and Bioinformatics. 79(3):735-751. PDF
Brylinski, M, Lee S Y, Zhou H, Skolnick J. 2011. The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF
Ando, T, Skolnick J. 2011. Brownian dynamics simulation of macromolecule diffusion in a protocell. Proceedings of the International Conference of the Quantum Bio-Informatics IV. 28:413-426. PDF
Guan, W, Ozakin A, Gray A, Borreguero J, Pandit S, Jagielska A, Wroblewska L, Skolnick J. 2011. Learning Protein Folding Energy Functions. 2011 IEEE 11th International Conference on Data Mining (ICDM)2011 IEEE 11th International Conference on Data Mining. :1062-1067. PDF
Brylinski, M, Gao M, Skolnick J. 2011. Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function Physical Chemistry Chemical Physics. 13 (38):17044-17055. PDF
2010
Ando, T, Skolnick J. 2010. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proceedings of the National Academy of Sciences of the United States of America. 107:18457-18462. PDF Supplementary Data
Gao, M, Skolnick J. 2010. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (Oxford, England). 26(18):2259-65. PDF Supplementary Data
Pandit, S B, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J. 2010. PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF
Zhou, H, Skolnick J. 2010. Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins. 78(9):2041-8. PDF
Brylinski, M, Skolnick J. 2010. Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins. 78(1):118-34. PDF Supplementary Data
Gao, M, Skolnick J. 2010. 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. 107(52):22517-22. PDF Supplementary Data
Brylinski, M, Skolnick J. 2010. Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. Journal of computational chemistry. 31(5):1093-105. PDF
Brylinski, M, Skolnick J. 2010. Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Molecular Pharmaceutics. 7(6):2324–2333. PDF
Brylinski, M, Skolnick J. 2010. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. Journal of Chemical Information and Modeling. 50:1839-1854. PDF
Pandit, S B, Zhou H, Skolnick J. 2010. TASSER-based protein structure prediction. Introduction to Protein Structure Prediction: Methods and Algorithms. 14:219-242. PDF
Pandit, S B, Skolnick J. 2010. TASSER_low-zsc: An approach to improve structure prediction using low z-score ranked templates. Protiens. 78(13):2769-2080. PDF
Lee, SY, Skolnick J. 2010. TASSER_WT: A protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets. Biophysical Journal. 99(9):3066-75. PDF Supplementary Data
2009
Skolnick, J, Brylinski M. 2009. Novel computational approaches to drug discovery. Proceedings of the International Conference of the Quantum Bio-Informatics III. PDF
Skolnick, J, Arakaki AK, Lee SY, Brylinski M. 2009. 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. 106(37):15690-5. PDF
Gao, M, Skolnick J. 2009. A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS computational biology. 5(11):e1000567. PDF Supplementary Data
Zhou, H, Skolnick J. 2009. Protein structure prediction by pro-Sp3-TASSER. Biophysical journal. 96(6):2119-27. PDF
Gao, M, Skolnick J. 2009. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS computational biology. 5(3):e1000341. PDF
Brylinski, M, Skolnick J. 2009. FINDSITE: a threading-based approach to ligand homology modeling. PLoS computational biology. 5(6):e1000405. PDF
Skolnick, J, Brylinski M. 2009. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings in bioinformatics. 10(4):378-91. PDF
Skolnick, J, Friesner RA. 2009. Theory and Simulation (Editorial overview). Current opinion in structural biology. 19(2):117-9. PDF
Arakaki, AK, Huang Y, Skolnick J. 2009. EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC bioinformatics. 10:107. PDF
Zhou, H, Pandit S B, Skolnick J. 2009. Performance of the Pro-sp3-TASSER server in CASP8. Proteins. 77 Suppl 9:123-7. PDF
Skolnick, J, Brylinski M, Lee SY. 2009. 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. PDF
2008
Arakaki, AK, Skolnick J, McDonald JF. 2008. Marker metabolites can be therapeutic targets as well. Nature. 456(7221):443. PDF
Zhou, H, Skolnick J. 2008. Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins. 71(3):1211-8. PDF
Jagielska, A, Wroblewska L, Skolnick J. 2008. 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. 105(24):8268-73. PDF
Kim, R, Skolnick J. 2008. Assessment of programs for ligand binding affinity prediction. Journal of computational chemistry. 29(8):1316-31. PDF
Brylinski, M, Skolnick J. 2008. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. Journal of computational chemistry. 29(10):1574-88. PDF Supplementary Data
Rotkiewicz, P, Skolnick J. 2008. Fast procedure for reconstruction of full-atom protein models from reduced representations. Journal of computational chemistry. 29(9):1460-5. PDF
Gao, M, Skolnick J. 2008. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic acids research. 36(12):3978-92. PDF Supplementary Data
Somarelli, JA, Lee SY, Skolnick J, Herrera RJ. 2008. Structure-based classification of 45 FK506-binding proteins. Proteins. 72(1):197-208. PDF
Brylinski, M, Skolnick J. 2008. 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. 105(1):129-34. PDF Supplementary Data
Chen, H, Skolnick J. 2008. M-TASSER: an algorithm for protein quaternary structure prediction. Biophysical journal. 94(3):918-28. PDF
Brylinski, M, Skolnick J. 2008. What is the relationship between the global structures of apo and holo proteins? Proteins. 70(2):363-77. PDF Supplementary Data
Lee, SY, Skolnick J. 2008. Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophysical journal. 95(4):1956-64. PDF
Wroblewska, L, Jagielska A, Skolnick J. 2008. Development of a physics-based force field for the scoring and refinement of protein models. Biophysical journal. 94(8):3227-40. PDF
Pandit, S B, Skolnick J. 2008. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC bioinformatics. 9:531. PDF
Arakaki, AK, Mezencev R, Bowen NJ, Huang Y, McDonald JF, Skolnick J. 2008. Identification of metabolites with anticancer properties by computational metabolomics. Molecular cancer. 7:57. PDF
Thomas, SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE. 2008. The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PloS one. 3(5):e2103. PDF