An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility

BMC Structural Biology

Volumn 13, Issue SUPPL.1, 2013, Pages

  Godshall, Brian G ^a   Tang, Yisheng ^a   Yang, Wenjie ^a   Chen, Brian Y ^a  

^a Lehigh University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABELSON KINASE; ENOLASE; MANDELATE RACEMASE; PROTEIN TYROSINE KINASE; VASODILATOR STIMULATED PHOSPHOPROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; BINDING SITE; CONFORMATIONAL TRANSITION; HUMAN; NONHUMAN; PREDICTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FAMILY; PROTEIN STRUCTURE;

ALGORITHMS; BINDING SITES; MODELS, MOLECULAR; PHOSPHOPYRUVATE HYDRATASE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN-TYROSINE KINASES; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84887460366     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-13-S1-S10     Document Type: Article

References (49)

1. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Barker JA, Thornton JM, Bioinformatics 2003 19 13 1644 1649 10.1093/bioinformatics/btg226 12967960
2. Algorithms for structural comparison and statistical analysis of 3D protein motifs. Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE, Pac Symp Biocomput 2005 345 334 45
3. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Nussinov R, Wolfson HJ, Proc Natl Acad Sci USA 1991 88 23 10495 9 10.1073/pnas.88.23.10495 1961713
4. SSAP: sequential structure alignment program for protein structure comparison. Orengo CA, Taylor WR, Methods Enzymol 1996 266 617 635 8743709
5. Mapping the protein universe. Holm L, Sander C, Science 1996 273 5275 595 603 10.1126/science.273.5275.595 8662544
6. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Shindyalov IN, Bourne PE, Protein Eng 1998 11 9 739 47 10.1093/protein/11.9.739 9796821
7. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Petrey D, Honig B, Methods Enzymol 2003 374 492 509 14696386
8. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Xie L, Bourne PE, Proc Natl Acad Sci USA 2008 105 14 5441 6 10.1073/pnas.0704422105 18385384
9. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. Russell RB, J Mol Biol 1998 279 5 1211 27 10.1006/jmbi.1998.1844 9642096
10. The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE, Journal of Computational Biology 2007 14 6 791 816 10.1089/cmb.2007.R017 17691895
11. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE, BMC Bioinformatics 2010 11 242 10.1186/1471-2105-11-242 20459833
12. Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins. Dundas J, Adamian L, Liang J, Journal of Molecular Biology 2011 406 5 713 729 http://www.ncbi.nlm.nih.gov/pubmed/21145898 10.1016/j.jmb.2010.12.005 21145898
13. Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE, Proceedings of The Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006) 2006 500 515
14. A Model for Statistical Significance of Local Similarities in Structure. Stark A, Sunyaev S, Russell RB, J Mol Biol 2003 326 1307 1316 10.1016/S0022-2836(03)00045-7 12595245
15. A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms. Fofanov V, Chen B, Bryant D, Moll M, Lichtarge O, Kavraki L, Kimmel M, 2008 IEEE International Conference on Bioinformatics and Biomeidcine Workshops 2008 1 8
16. VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. Chen BY, Honig B, PLoS Comput Biol 2010 6 8 ii: e1000881 20814581
17. A Statistical Model of Overlapping Volume in Ligand Binding Cavities. Chen B, Bandyopadhyay S, Proceedings of the Computational Structural Bioinformatics Workshop (CSBW 2011) 2011 424 31
18. VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity. Chen B, Bandyopadhyay S, Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2011 22 9
19. Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass. Pasternak O, Biesiadka J, Dolot R, Handschuh L, Bujacz G, Sikorski MM, Jaskolski M, Acta Crystallogr D Biol Crystallogr 2005 61 99 107 10.1107/S0907444904028173 15608381
20. Improving accuracy in binding site comparison with homology modeling. Godshall B, Chen B, Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on: 4-7 October 2012 2012 662 669 10.1109/BIBMW.2012. 6470291
21. A brighter future for protein structure prediction. Koehl P, Levitt M, et al. Nature Structural Biology 1999 6 108 111 10.1038/5794 10048917
22. Protein structure prediction and structural genomics. Baker D, Sali A, Science's STKE 2001 294 5540 93 24069623
23. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. Yang AS, Honig B, J Mol Biol 2000 301 3 665 78 10.1006/jmbi.2000.3973 10966776
24. The LabelHash algorithm for substructure matching. Moll M, Bryant DH, Kavraki LE, BMC Bioinformatics 2010 11 555 10.1186/1471-2105-11-555 21070651
25. Recognition of Binding Patterns Common to a Set of Protein Structures. Shatsky M, Shulman-peleg A, Nussinov R, Wolfson HJ, Lect Notes Comput Sc 2005 3500 440 455 10.1007/11415770-33
26. A NewMethod to Detect Related Function Among Proteins Independent of Sequence and Fold Homology. Schmitt S, Kuhn D, Klebe G, J Mol Biol 2002 323 2 387 406 10.1016/S0022-2836(02)00811-2 12381328
27. The Protein Data Bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 235 42 10.1093/nar/28.1.235 10592235
28. FlexProt: alignment of flexible protein structures without a predefinition of hinge regions. Shatsky M, Nussinov R, Wolfson HJ, J Comput Biol 2004 11 83 106 10.1089/106652704773416902 15072690
29. FlexSnap: Flexible Non-sequential Protein Structure Alignment. Salem S, Zaki M, Bystroff C, Algorithms for Molecular Biology 2010 5 12 10.1186/1748-7188-5-12 20047669
30. Multiple flexible structure alignment using partial order graphs. Ye Y, Godzik A, Bioinformatics 2005 21 10 2362 9 10.1093/bioinformatics/bti353 15746292
31. Extending the accuracy limits of prediction for side-chain conformations1. Xiang Z, Honig B, Journal of molecular biology 2001 311 2 421 430 10.1006/jmbi.2001.4865 11478870
32. A new bioinformatics analysis tools framework at EMBL-EBI. Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R, Nucleic acids research 2010 38 suppl 2 695 W699 20439314
33. The interpretation of protein structures: estimation of static accessibility. Lee B, Richards FM, J Mol Biol 1971 55 3 379 400 10.1016/0022-2836(71)90324-X 5551392
34. Solvent-accessible surfaces of proteins and nucleic acids. Connolly M, Science 1983 221 4612 709 713 10.1126/science.6879170 6879170
35. On the Nature of Cavities on Protein Surfaces: Application to the Identification of Drug-Binding Sites. Nayal M, Honig B, Proteins Struct Funct Genet 2006 63 892 906 10.1002/prot.20897 16477622
36. Modeling regionalized volumetric differences in protein-ligand binding cavities. Chen BY, Bandyopadhyay S, Proteome Science 2012 10 Suppl 1 6 10.1186/1477-5956-10-S1-S6 22759583
37. Face traverses and a volume algorithm for polyhedra. Schaer J, Stone M, Lect Notes Comput Sc 1991 555/1991 290 297
38. A regionalizable statistical model of intersecting regions in protein ligand binding cavities. Chen BY, Bandyopadhyay S, Journal of Bioinformatics and Computational Biology 2012 10 3 1242004 10.1142/S0219720012420048 22809380
39. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA, Biochemistry 2008 47 38 9944 54 10.1021/bi800914r 18754693
40. The P-loop-a common motif in ATP-and GTP-binding proteins. Saraste M, Sibbald P, Wittinghofer A, et al. Trends in biochemical sciences 1990 15 11 430 10.1016/0968-0004(90)90281-F 2126155
41. A conserved protonation-dependent switch controls drug binding in the Abl kinase. Shan Y, Seeliger M, Eastwood M, Frank F, Xu H, Jensen M, Dror R, Kuriyan J, Shaw D, Proc Natl Acad Sci USA 2009 106 139 144 10.1073/pnas. 0811223106 19109437
42. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA, Biochemistry 1996 35 51 16489 501 10.1021/bi9616413 8987982
43. Crystal structure of the Escherichia coli RNA degradosome component enolase. Kühnel K, Luisi BF, J Mol Biol 2001 313 3 583 92 10.1006/jmbi.2001.5065 11676541
44. Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant. Schafer SL, Barrett WC, Kallarakal AT, Mitra B, Kozarich JW, Gerlt JA, Clifton JG, Petsko GA, Kenyon GL, Biochemistry 1996 35 18 5662 9 10.1021/bi960174m 8639525
45. Catalytic specificity of protein-tyrosine kinases is critical for selective signalling. Songyang Z, Carraway K, Eck M, Harrison S, Feldman R, Mohammadi M, Schlessinger J, Hubbard S, Smith D, Eng C, et al. Nature 1995 373 6514 536 539 10.1038/373536a0 7845468
46. Tyrosine kinases as targets for cancer therapy. Krause D, Van Etten R, New England Journal of Medicine 2005 353 2 172 187 10.1056/NEJMra044389 16014887
47. The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Deininger M, Buchdunger E, Druker B, Blood 2005 105 7 2640 2653 10.1182/blood-2004-08-3097 15618470
48. A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src. Liu Y, Shah K, Yang F, Witucki L, Shokat KM, Bioorganic & medicinal chemistry 1998 6 8 1219 26 10.1016/S0968-0896(98)00099-6 24066705
49. Targeting the gatekeeper residue in phosphoinositide 3-kinases. Alaimo PJ, Knight Za, Shokat KM, Bioorganic & medicinal chemistry 2005 13 8 2825 36 10.1016/j.bmc.2005.02.021 24066705