Jeffrey Skolnick

Summary

Affiliation: Georgia Institute of Technology
Country: USA

Publications

  1. pmc From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS Comput Biol 5:e1000341. 2009
  2. pmc FINDSITE: a threading-based approach to ligand homology modeling
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS Comput Biol 5:e1000405. 2009
  3. pmc DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Nucleic Acids Res 36:3978-92. 2008
  4. pmc A threading-based method for the prediction of DNA-binding proteins with application to the human genome
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    PLoS Comput Biol 5:e1000567. 2009
  5. pmc Interplay of physics and evolution in the likely origin of protein biochemical function
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 110:9344-9. 2013
  6. pmc Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Curr Opin Struct Biol 23:191-7. 2013
  7. pmc Further evidence for the likely completeness of the library of solved single domain protein structures
    Jeffrey Skolnick
    Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA
    J Phys Chem B 116:6654-64. 2012
  8. pmc Ab initio modeling of small proteins by iterative TASSER simulations
    Sitao Wu
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
    BMC Biol 5:17. 2007
  9. pmc The continuity of protein structure space is an intrinsic property of proteins
    Jeffrey Skolnick
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 106:15690-5. 2009
  10. pmc FINDSITE: a combined evolution/structure-based approach to protein function prediction
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th St NW, Atlanta, GA 30318, USA
    Brief Bioinform 10:378-91. 2009

Collaborators

Detail Information

Publications62

  1. pmc From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS Comput Biol 5:e1000341. 2009
    ..The similarity between the specific DNA-protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein...
  2. pmc FINDSITE: a threading-based approach to ligand homology modeling
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS Comput Biol 5:e1000405. 2009
    ..Thus, the rather accurate, computationally inexpensive FINDSITE(LHM) algorithm should be a useful approach to assist in the discovery of novel biopharmaceuticals...
  3. pmc DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Nucleic Acids Res 36:3978-92. 2008
    ..DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/...
  4. pmc A threading-based method for the prediction of DNA-binding proteins with application to the human genome
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    PLoS Comput Biol 5:e1000567. 2009
    ..Finally, we present some interesting predictions in detail. In particular, it is estimated that approximately 20% of classic zinc finger domains play a functional role not related to direct DNA-binding...
  5. pmc Interplay of physics and evolution in the likely origin of protein biochemical function
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 110:9344-9. 2013
    ....
  6. pmc Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Curr Opin Struct Biol 23:191-7. 2013
    ..Thus, despite the widespread belief to the contrary, low-to-moderate resolution predicted structures have considerable utility for biochemical function prediction...
  7. pmc Further evidence for the likely completeness of the library of solved single domain protein structures
    Jeffrey Skolnick
    Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA
    J Phys Chem B 116:6654-64. 2012
    ..45 (0.5) TM-score threshold, essentially all (most) are found in the PDB. Thus, the conclusion that the PDB is likely complete is further supported...
  8. pmc Ab initio modeling of small proteins by iterative TASSER simulations
    Sitao Wu
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
    BMC Biol 5:17. 2007
    ..The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins...
  9. pmc The continuity of protein structure space is an intrinsic property of proteins
    Jeffrey Skolnick
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 106:15690-5. 2009
    ....
  10. pmc FINDSITE: a combined evolution/structure-based approach to protein function prediction
    Jeffrey Skolnick
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th St NW, Atlanta, GA 30318, USA
    Brief Bioinform 10:378-91. 2009
    ..Importantly, FINDSITE gives comparable results when high-resolution experimental structures as well as predicted protein models are used...
  11. pmc Ab initio protein structure prediction using chunk-TASSER
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Biophys J 93:1510-8. 2007
    ..Chunk-TASSER is approximately 11% (10%) better than TASSER for the total TM-score of the first (best of top five) models. Chunk-TASSER is fully automated and can be used in proteome scale protein structure prediction...
  12. pmc A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 105:129-34. 2008
    ..Furthermore, the chemical properties of template-bound ligands can be used to select ligand templates associated with the binding site. In most cases, FINDSITE can accurately assign a molecular function to the protein model...
  13. pmc Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
    Shashi Bhushan Pandit
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA
    BMC Bioinformatics 9:531. 2008
    ....
  14. pmc Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints
    Seung Yup Lee
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Biophys J 95:1956-64. 2008
    ..3% (64.7%) and 40.8% (35.5%) for the Hard targets (incorrect templates/alignments). For Easy targets (good templates/alignments), the success rate slightly increases from 86.3% to 88.4%...
  15. pmc PSiFR: an integrated resource for prediction of protein structure and function
    Shashi B Pandit
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Bioinformatics 26:687-8. 2010
    ....
  16. pmc APoc: large-scale identification of similar protein pockets
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30076, USA
    Bioinformatics 29:597-604. 2013
    ..An efficient method for comparing these pockets could greatly assist the classification of ligand-binding sites, prediction of protein molecular function and design of novel drug compounds...
  17. pmc The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement
    Michal Brylinski
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    J Struct Biol 173:558-69. 2011
    ..The Binding Site Refinement (BSR) approach is available to the scientific community as a web server that can be accessed at http://cssb.biology.gatech.edu/bsr/...
  18. pmc Comparison of structure-based and threading-based approaches to protein functional annotation
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Proteins 78:118-34. 2010
    ..Combined evolution/structure-based function assignment emerges as a powerful technique that can make a significant contribution to comprehensive proteome annotation...
  19. pmc Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA
    J Comput Chem 29:1574-88. 2008
    ..The success rate of Q-Dock employing a pocket-specific potential is 6.3 times higher than that previously reported for the Dolores method, another low-resolution docking approach...
  20. pmc The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 109:3784-9. 2012
    ..We propose that packing nearby protein-protein or domain-domain interfaces is a major route to the formation of ligand-binding pockets...
  21. pmc New benchmark metrics for protein-protein docking methods
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 79:1623-34. 2011
    ..While the results according to the new scoring scheme are generally consistent with the original CAPRI assessment, the IS-score identifies models whose significance was previously underestimated...
  22. pmc Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    J Chem Inf Model 50:1839-54. 2010
    ..biology.gatech.edu/kinomelhm/ as well as at the ZINC Web site ( http://zinc.docking.org/applications/2010Apr/Brylinski-2010.tar.gz )...
  23. pmc TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets
    Seung Yup Lee
    Center for Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Biophys J 99:3066-75. 2010
    ..4, when F(wt ≥ 3)(cov) > 1.0 and > 0.4, the success rate of TASSER_WT (TASSER_2.0) is 98.8% (76.2%) and 93.7% (81.1%), respectively...
  24. ncbi request reprint Analysis of TASSER-based CASP7 protein structure prediction results
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 69:90-7. 2007
    ..For the more difficult targets, TASSER with modest human intervention performed better in comparison to its server counterpart, MetaTASSER, which used a limited time simulation...
  25. pmc A comprehensive survey of small-molecule binding pockets in proteins
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS Comput Biol 9:e1003302. 2013
    ..Finally, we discuss the implications of our study for the prediction of protein-ligand interactions based on pocket comparison. ..
  26. pmc Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 78:2041-8. 2010
    ..Moreover, the number of foldable targets (TM-score >or= 0.4) increases from least 7.6% for SP(3) to 54% for SPARKS. Thus, FTCOM is a promising approach to template selection. Proteins 2010. (c) 2010 Wiley-Liss, Inc...
  27. pmc Performance of the Pro-sp3-TASSER server in CASP8
    Hongyi Zhou
    Center for Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 77:123-7. 2009
    ..Finally, we analyze the overall performance and highlight some successful predictions of the pro-sp3-TASSER server...
  28. pmc Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function
    Michal Brylinski
    Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St NW, Atlanta, GA 30076, USA
    Phys Chem Chem Phys 13:17044-55. 2011
    ....
  29. pmc Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 107:22517-22. 2010
    ..Finally, our results provide a structural explanation for the prevalence of promiscuous protein interactions. By side-chain packing adjustments, we illustrate how multiprotein specificity can be attained at a promiscuous interface...
  30. pmc iAlign: a method for the structural comparison of protein-protein interfaces
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Bioinformatics 26:2259-65. 2010
    ..While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein-protein complexes...
  31. ncbi request reprint Benchmarking of TASSER in the ab initio limit
    Jose M Borreguero
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 68:48-56. 2007
    ..Thus, it is the effective configurational entropy of the protein that dictates the average likelihood of correctly arranging the secondary structure elements...
  32. pmc Development of a physics-based force field for the scoring and refinement of protein models
    Liliana Wroblewska
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Biophys J 94:3227-40. 2008
    ..For a set of seven proteins, 63% of the decoys improve, 18% get worse, and 19% are not changed...
  33. pmc M-TASSER: an algorithm for protein quaternary structure prediction
    Huiling Chen
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Biophys J 94:918-28. 2008
    ..Thus, we have developed a promising approach to predict full-length quaternary structure for proteins that have weak sequence similarity to proteins of solved quaternary structure...
  34. pmc FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, N W, Atlanta, Georgia 30318, USA
    J Chem Inf Model 53:230-40. 2013
    ..The FINDSITE(comb) web service is freely available for academic users at http://cssb.biology.gatech.edu/skolnick/webservice/FINDSITE-COMB/index.html...
  35. pmc FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level
    Michal Brylinski
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 79:735-51. 2011
    ..FINDSITE-metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite-metal/...
  36. pmc TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates
    Shashi B Pandit
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 78:2769-80. 2010
    ..Similar improvements are observed with low-ranked templates from SPARKS(2). The template clustering approach could be applied to other modeling methods that utilize multiple templates to improve structure prediction...
  37. pmc Protein structure prediction by pro-Sp3-TASSER
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Biophys J 96:2119-27. 2009
    ..A server that implements the above algorithm is available at http://cssb.biology.gatech.edu/skolnick/webservice/pro-sp3-TASSER/. The source code is also available upon request...
  38. pmc TASSER-Lite: an automated tool for protein comparative modeling
    Shashi Bhushan Pandit
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Biophys J 91:4180-90. 2006
    ..TASSER-Lite is provided on the web at (http://cssb.biology.gatech.edu/skolnick/webservice/tasserlite/index.html)...
  39. pmc Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 71:1211-8. 2008
    ..83 for the 98 targets, which is better than those of other quality assessment methods that participated in CASP7. Our method also outperforms the other methods by about 3% as assessed by the total GDT-score of the selected top models...
  40. pmc EFICAz2: enzyme function inference by a combined approach enhanced by machine learning
    Adrian K Arakaki
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    BMC Bioinformatics 10:107. 2009
    ..To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment...
  41. pmc Assessment of programs for ligand binding affinity prediction
    RyangGuk Kim
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, Atlanta, Georgia 30318, USA
    J Comput Chem 29:1316-31. 2008
    ....
  42. pmc Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA
    J Comput Chem 31:1093-105. 2010
    ....
  43. ncbi request reprint What is the relationship between the global structures of apo and holo proteins?
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 70:363-77. 2008
    ..These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited...
  44. pmc Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach
    Michal Brylinski
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Mol Pharm 7:2324-33. 2010
    ..The constructed cross-reactivity profiles for the human kinome are freely available to the academic community at http://cssb.biology.gatech.edu/kinomelhm/ ...
  45. ncbi request reprint Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions
    Seung Yup Lee
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    Proteins 68:39-47. 2007
    ..6 to 84.0%. These results suggest that TASSER(iter) can provide more reliable predictions for targets of Medium difficulty, a range that had resisted improvement in the quality of protein structure predictions...
  46. pmc Protein model refinement using an optimized physics-based all-atom force field
    Anna Jagielska
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Proc Natl Acad Sci U S A 105:8268-73. 2008
    ..The ability to do such systematic structural refinements by using a physics-based all-atom potential represents a promising approach to high-resolution structure prediction...
  47. pmc The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria
    Sara H Thomas
    School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS ONE 3:e2103. 2008
    ..The mosaic nature of the A. dehalogenans strain 2CP-C genome suggests that the metabolically versatile, anaerobic members of the delta-Proteobacteria may have descended from aerobic ancestors with complex lifestyles...
  48. pmc EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes
    Narendra Kumar
    Center for Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
    Bioinformatics 28:2687-8. 2012
    ..5), that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz(2.5) to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database...
  49. pmc GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Biophys J 101:2043-52. 2011
    ..Thus, GOAP is a promising advance in knowledge-based, all-atom statistical potentials. GOAP is available for download at http://cssb.biology.gatech.edu/GOAP...
  50. pmc Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations
    Tadashi Ando
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318 5304, USA
    J Chem Phys 139:121922. 2013
    ..The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. ..
  51. ncbi request reprint Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field
    Anna Jagielska
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, Atlanta, Georgia 30318, USA
    J Comput Chem 28:1648-57. 2007
    ..Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-extended state energetics and geometry of major conformations...
  52. ncbi request reprint Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
    Liliana Wroblewska
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    J Comput Chem 28:2059-66. 2007
    ..Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed...
  53. pmc High precision multi-genome scale reannotation of enzyme function by EFICAz
    Adrian K Arakaki
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
    BMC Genomics 7:315. 2006
    ..We have performed a reannotation of 245 genomes using an updated version of EFICAz, a highly precise method for enzyme function prediction...
  54. pmc On the importance of hydrodynamic interactions in lipid membrane formation
    Tadashi Ando
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Biophys J 104:96-105. 2013
    ..These results clearly suggest that HI greatly affects the kinetics of self-assembly and that simulations without HI will significantly underestimate the kinetic parameters of such processes...
  55. pmc Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations
    Tadashi Ando
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318 5304, USA
    J Chem Phys 137:064106. 2012
    ..Thus, Krylov subspace methods are recommended for performing large-scale brownian dynamics simulations with hydrodynamic interactions...
  56. pmc FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs
    Hongyi Zhou
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, N W, Atlanta, Georgia 30318, United States
    Mol Pharm 9:1775-84. 2012
    ..All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html ...
  57. pmc Identification of metabolites with anticancer properties by computational metabolomics
    Adrian K Arakaki
    Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Mol Cancer 7:57. 2008
    ..The fact that metabolites can affect the cancer process on so many levels suggests that the change in concentration of some metabolites that occurs in cancer cells could have an active role in the progress of the disease...
  58. ncbi request reprint Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils
    Robert J Martinez
    School of Biology, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA
    Environ Microbiol 9:3122-33. 2007
    ..This study provides the first evidence of U(VI) precipitation via the phosphatase activity of naturally occurring Bacillus and Rahnella spp. isolated from the acidic subsurface at the DOE ORFRC...
  59. ncbi request reprint Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
    Adrian K Arakaki
    Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203 1199, USA
    Bioinformatics 20:1087-96. 2004
    ..These methods are successful when applied to high-resolution structures, but their detection ability in lower resolution predicted structures has only been tested for a few cases...
  60. ncbi request reprint How well is enzyme function conserved as a function of pairwise sequence identity?
    Weidong Tian
    Center of Excellence in Bioinformatics, University at Buffalo, The State University of New York, 901 Washington Street, Buffalo, NY 14203, USA
    J Mol Biol 333:863-82. 2003
    ..However, this comes at a cost: those true positive sequences below this threshold cannot be uniquely identified...
  61. ncbi request reprint MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading
    Long Lu
    Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
    Proteins 49:350-64. 2002
    ..An estimation of the false-negative rate for yeast-predicted interactions has also been provided. Thus, a promising approach to help assist in the assignment of protein-protein interactions on a genomic scale has been developed...
  62. pmc EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
    Weidong Tian
    Center of Excellence in Bioinformatics, University at Buffalo, The State University of New York, 901 Washington Street, Buffalo, NY 14203 1199, USA
    Nucleic Acids Res 32:6226-39. 2004
    ..Applied to Escherichia coli genome, EFICAz assigns more detailed enzymatic function than KEGG, and generates numerous novel predictions...

Research Grants25

  1. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 1999
    ..abstract_text> ..
  2. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2006
    ..7). The algorithms developed in Specific Aims 1-6 will be applied to over 100 proteomes including human. We will model human GPCRs, kinases, proteases and phosphatases. ..
  3. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2006
    ..The overall goal is to range of validity of our ab initio folding algorithms and to provide significant improvements in the state of the art of tertiary structure prediction. ..
  4. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2007
    ..7). The algorithms developed in Specific Aims 1-6 will be applied to over 100 proteomes including human. We will model human GPCRs, kinases, proteases and phosphatases. ..
  5. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2005
    ..The overall goal is to range of validity of our ab initio folding algorithms and to provide significant improvements in the state of the art of tertiary structure prediction. ..
  6. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2007
    ..For all Specific Aims, comprehensive benchmarking that includes participation in future CASPs will be done. All developed algorithms, tools, and results will be made available on our website, http://cssb.biology.gatech.edu/skolnick/. ..
  7. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2009
    ..Also, most of the estimated 650,000 protein-protein interactions in the human interactome are unknown; by providing predicted protein quaternary structures, insights into how these proteins perform their function will result. ..
  8. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2009
    ..All developed algorithms, tools, and results will be made available on our website, http://cssb.biology.gatech.edu/skolnick/. ..
  9. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2010
    ..Also, most of the estimated 650,000 protein-protein interactions in the human interactome are unknown;by providing predicted protein quaternary structures, insights into how these proteins perform their function will result. ..
  10. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2005
    ..The overall goal is to range of validity of our ab initio folding algorithms and to provide significant improvements in the state of the art of tertiary structure prediction. ..
  11. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2005
    ..7). The algorithms developed in Specific Aims 1-6 will be applied to over 100 proteomes including human. We will model human GPCRs, kinases, proteases and phosphatases. ..
  12. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2004
    ..The overall goal is to range of validity of our ab initio folding algorithms and to provide significant improvements in the state of the art of tertiary structure prediction. ..
  13. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 1999
    ..Thus, a robust protocol capable of handling the plethora of sequences provided by the human genome project will be developed. ..
  14. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2000
    ..Thus, a robust protocol capable of handling the plethora of sequences provided by the human genome project will be developed. ..
  15. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2000
    ..abstract_text> ..
  16. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2001
    ..cerevisiae, C. elegans and human. (5) A structure-function database of fold/function prediction of these five genomes will be constructed and will be available on a website (http://bioinformatics.danforthcenter.org). ..
  17. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2001
    ..abstract_text> ..
  18. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2002
    ..cerevisiae, C. elegans and human. (5) A structure-function database of fold/function prediction of these five genomes will be constructed and will be available on a website (http://bioinformatics.danforthcenter.org). ..
  19. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2002
    ..abstract_text> ..
  20. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2003
    ..cerevisiae, C. elegans and human. (5) A structure-function database of fold/function prediction of these five genomes will be constructed and will be available on a website (http://bioinformatics.danforthcenter.org). ..
  21. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2003
    ..The overall goal is to range of validity of our ab initio folding algorithms and to provide significant improvements in the state of the art of tertiary structure prediction. ..
  22. INTERACTION PATTERN BASED PREDICTOR OF PROTEIN STRUCTURE
    Jeffrey Skolnick; Fiscal Year: 2004
    ..cerevisiae, C. elegans and human. (5) A structure-function database of fold/function prediction of these five genomes will be constructed and will be available on a website (http://bioinformatics.danforthcenter.org). ..
  23. COMPUTER SIMULATION THEORY OF GLOBULAR PROTEIN DYNAMICS
    Jeffrey Skolnick; Fiscal Year: 2010
    ..All developed algorithms, tools, and results will be made available on our website, http://cssb.biology.gatech.edu/skolnick/. ..