Jeffrey Skolnick, Professor; Director, Center for the Study of Systems Biology; GRA Eminent Scholar
Ph.D., Yale University, 1977
Phone: (404) 407-8975
Fax: (404) 385-7478
Office: GTRI, 250 14th Street, NW, Room 138
Research Interests
Computational Biology, Bioinformatics, and Systems Biology - Development of tools for the prediction of protein structure and function from sequence; functional genomics; automatic assignment of enzymes to metabolic pathways, prediction of protein tertiary and quaternary structure and folding pathways; prediction of membrane protein tertiary structure, prediction of small molecule ligands for drug discovery, prediction of druggable protein targets, drug design, equilibrium and dynamic properties of lipid bilayers; simulation of virus coat protein assembly.
Selected Publications
1. 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.
2. D. Kihara and J. Skolnick. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins 2004:55: 464-473.
3. J. Skolnick, D. Kihara and Y. Zhang. Development and testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004:56: 502-518.
4. 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.
5. Y. Zhang and J. Skolnick. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Science 2004:101: 7594-7599.
6. J. Skolnick. What practical use is protein structure prediction to drug discovery? BioIt World, Commentary, October 10, 2003.
7. Y. Zhang and J. Skolnick. SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem. 2004:25: 865-871.
8. 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.
9. Y. Zhang and J. Skolnick. A scoring function for the automated assessment of protein structure template quality. Proteins 2004:57: 702-710.
10. W. Li, Y. Zhang and J. Skolnick. Application of sparse NMR restraints to large-scale protein structure prediction. Biophysical Journal 2004:87: 241-1248.
11. M. Betancourt and J. Skolnick. Local propensities and statistical potentials of backbone dihedral angles in proteins. Journal of Molecular Biology 2004: 342: 635-649.
12. Y. Zhang and J. Skolnick. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophysical Journal 2004: 87: 2647-2655.
13. E. Bindewald and J. Skolnick. A scoring function for docking ligands to low-resolution protein structures. Journal of Computational Chemistry 2005:26: 374-383.
14. 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.
15. A. Szilagyi, V. Grimm, A. Arakaki and J. Skolnick. Prediction of protein-protein interactions. Physical Biology 2005:(2): S1-S16.
16. Y. Zhang and J. Skolnick. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Computational Biology 2006:2(2): 88-99.
17. J. Skolnick. Putting the pathway back into protein folding. Proc Natl Acad Science 2005:102(7): 2265-2266.
18. Y. Zhang and J. Skolnick. TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 2005: 33: 2302-2309.
19. Y. Zhang and J. Skolnick. TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005:61(S7): 91-98.
20. 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.