Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9

Journal of Bioinformatics and Computational Biology

Volumn 10, Issue 3, 2012, Pages

  Cheng, Jianlin ^a,b   Eickholt, Jesse ^a   Wang, Zheng ^a,b   Deng, Xin ^a  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

CASP; Protein structure prediction; recursive protein modeling; template based modeling; template free modeling

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84862507501     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720012420036     Document Type: Conference Paper

References (60)

1. Chen BY, Honig B, VASP: A volumetric analysis of surface properties yields insights into protein-ligand binding specicity, PLoS Comput Biol 6(8):11, 2010.
2. Nalam MNL, Ali A, Altman MD, Reddy GSKK, Cao H, Gilson MK, Tidor B, Rana TM, Schi®er CA, Evaluating the substrate-envelope hypothesis: Structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance, J Virol 84(10):5368-5378, 2010.
3. Frey K, Georgiev I, Donald B, Anderson A, Predicting resistance mutations using protein design algorithms, Proc. Natl. Acad. Sci. USA 107(31):13707-13712, 2010.
4. Chen B, Bandyopadhyay S, VASP-S: A volumetric analysis and statistical model for predicting steric in̊uences on protein-ligand binding specicity, Proc 2011 IEEE Int Conf Bioinform Biomed (BIBM), pp. 22-9, 2011.
5. Chen B, Bandyopadhyay S, A statistical model of overlapping volume in ligand binding cavities, Proc Comput Struct Bioinform Workshop (CSBW 2011), pp. 424-431, 2011.
6. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE, The MASH pipeline for protein function prediction and an algorithm for the geometric renement of 3D motifs, J Comput Biol 14(6):791-816, 2007.
7. Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O, Prediction of enzyme function based on 3D templates of evolutionarily important amino acids, BMC Bioinformatics 9:17, 2008.
8. Umeyama S, Least-squares estimation of transformation parameters between two point patterns, IEEE Trans Pattern Analysis and Machine Intelligence 13(4):376-380, 1991.
9. Nussinov R, Wolfson HJ, Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques, Proc. Natl. Acad. Sci. USA 88(23):10495-10499, 1991.
10. Orengo CA, Taylor WR, SSAP: Sequential structure alignment program for protein structure comparison, Method Enzymol 266:617-635, 1996.
11. Shindyalov IN, Bourne PE, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11(9):739-747, 1998.
12. Petrey D, Honig B, GRASP2: Visualization, surface properties, and electrostatics of macromolecular structures and sequences, Method Enzymol 374(1991):492-509, 2003.
13. Yang A-S Honig B, 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, J Mol Biol 301(3):665-678, 2000.
14. Holm L, Sander C, Mapping the protein universe, Science 273(5275):595-603, 1996.
15. Gibrat JF, Madej T, Bryant SH, Surprising similarities in structure comparison, Curr Opin Struct Biol 6(3):377-385, 1996.
16. Xie L, Bourne PE, Detecting evolutionary relationships across existing fold space, using sequence order-independent prole-prole alignments, Proc. Natl. Acad. Sci. USA 105(14):5441-5446, 2008.
17. Ye Y, Godzik A, Flexible structure alignment by chaining aligned fragment pairs allowing twists, Bioinformatics 19(90002) Suppl(2):ii246-i255, 2003.
18. Shatsky M, Nussinov R, Wolfson HJ, FlexProt: Alignment of ̊exible protein structures without a predenition of hinge regions, J Comput Biol 11(1):83-106, 2004.
19. Ye Y, Godzik A, Multiple ̊exible structure alignment using partial order graphs, Bioinformatics 21(10):2362-2369, 2005.
20. Kolodny R, Petrey D, Honig B, Protein structure comparison: Implications for the nature of ̀fold space', and structure and function prediction, Curr Opin Struct Biol 16(3):393-398, 2006.
21. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM, CATH-A hierarchic classication of protein domain structures, Structure 5(8):1093-1108, 1997.
22. Krishna SS, Grishin NV, Structural drift: A possible path to protein fold change, Bioinformatics 21(8):1308-1310, 2005.
23. Petrey D, Honig B, Is protein classication necessary? Towards alternative approaches to function annotation, Curr Opin Struct Biol 19(3):363-368, 2009.
24. Russell RB, Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution, J Mol Biol 279(5):1211-1227, 1998.
25. Barker JA, Thornton JM, An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis, Bioinformatics 19(13):1644-1649, 2003.
26. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE, The MASH pipeline for protein function prediction and an algorithm for the geometric renement of 3D motifs, J. Comput. Biol. 14(6):791-816, 2007.
27. Polacco BJ, Babbitt PC, Automated discovery of 3D motifs for protein function annotation, Bioinformatics 22(6):723-730, 2006. Available: Http://www.ncbi.nlm.nih.gov/pubmed/16410325.
28. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE, Geometric sieving: Automated distributed optimization of 3D motifs for protein function prediction, Proc Tenth Annual Int. Conf. Computational Molecular Biology (RECOMB 2006), pp. 500-515, 2006.
29. Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE, Composite motifs integrating multiple protein structures increase sensitivity for function prediction, Comput Syst Bioinformatics Conf 6:343-355, 2007.
30. Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE, Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction, BMC Bioinformatics 11:242, 2010.
31. Dundas J, Adamian L, Liang J, Structural signatures of enzyme binding pockets from order-independent surface alignment: A study of metalloendopeptidase and nad binding proteins, J Mol Biol 406(5):713-729, 2011. Available: Http://www.ncbi.nlm.nih.gov/pubmed/21145898.
32. Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE, Cavity-Aware motifs reduce false positives in protein function prediction, Proc 2006 IEEE Comput Syst Bioinformatics Conference (CSB 2006), pp. 311-323, 2006.
33. Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE, Cavity scaling: Automated renement of cavity-Aware motifs in protein function prediction, J Bioinform Comput Biol 5(2a):353-382, 2007.
34. Lee B, Richards FM, The interpretation of protein structures: Estimation of static accessibility, J Mol Biol 55(3):379-400, 1971.
35. Connolly M, Solvent-Accessible surfaces of proteins and nucleic acids, Science 221(4612):709-713, 1983.
36. Rosen M, Lin SL, Wolfson H, Nussinov R, Molecular shape comparisons in searches for active sites and functional similarity, Protein Eng 11(4):263-277, 1998.
37. Kinoshita K, Nakamura H, Identication of the ligand binding sites on the molecular surface of proteins, Protein Sci 14:711-718, 2005.
38. Laskowski RA, SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions, J Mol Graph 13(5):323-330, 307-308, 1995.
39. Binkowski TA, CASTp: Computed atlas of surface topography of proteins, Nucleic Acids Res 31(13):3352-3355, 2003.
40. Binkowski TA, Adamian L, Liang J, Inferring functional relationships of proteins from local sequence and spatial surface patterns, J Mol Biol 332(2):505-526, 2003.
41. Binkowski TA, Joachimiak A, Protein functional surfaces: Global shape matching and local spatial alignments of ligand binding sites, BMC Struct Biol 8:45, 2008.
42. Ritchie DW, Kemp GJL, Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces, J Comput Chem 20(4):383, 1999.
43. Kazhdan M, Funkhouser T, Rusinkiewicz S, Rotation invariant spherical harmonic representation of 3D shape descriptors, European Symposium on Geometry Processing 2003, 2003.
44. Kahraman A, Morris RJ, Laskowski RA, Thornton JM, Shape variation in protein binding pockets and their ligands, J Mol Biol 368(1):283-301, 2007.
45. Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA, Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absense of global structural similarity, Multiscale Model Simul 5(4):1196-1213, 2006.
46. Nayal M, Honig B, On the nature of cavities on protein surfaces: Application to the identication of drug-binding sites, Proteins: Struct Funct Genet 63:892-906, 2006.
47. Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM, A method for localizing ligand binding pockets in protein structures, Proteins: Struct Funct Bioinf 62(2):479-488, 2006.
48. Coleman RG, Sharp KA, Travel depth, a new shape descriptor for macromolecules: Application to ligand binding, J Mol Biol 362(3):441-458, 2006.
49. Bogan AA, Thorn KS, Anatomy of hot spots in protein interfaces, J Mol Biol 280(1):1-9, 1998.
50. Stark A, Sunyaev S, Russell RB, A model for statistical signicance of local similarities in structure, J Mol Biol 326:1307-1316, 2003.
51. Chen CP, Posy S, Ben-Shaul A, Shapiro L, Honig B, Specicity of cell-cell adhesion by classical cadherins: Critical role for low-Affinity dimerization through beta-strand swapping, Proc. Natl. Acad. Sci. USA 102(24):8531-8536, 2005.
52. Schaer J, Stone M, Face traverses and a volume algorithm for polyhedra, Lecture Notes on Comput Science 555(1991):290-297, 1991.
53. Morihara K, Tsuzuki H, Comparison of the specicities of various serine proteinases from microorganisms, Arch Biochem Biophys 129(2):620-634, 1969.
54. Gr-Af L, Jancs-o A, Szil-Agyi L, Hegyi G, Pint-er K, N-Aray-Szab-o G, Hepp J, Medzihradszky K, Rutter WJ, Electrostatic complementarity within the substrate-binding pocket of trypsin, Proc. Natl. Acad. Sci. USA 85(14):4961-4965, 1988.
55. Berglund GI, Smalas AO, Outzen H, Willassen NP, Purication and characterization of pancreatic elastase from North Atlantic salmon (Salmo salar), Mol Mar Biol Biotechnol 7(2):105-114, 1998.
56. Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA, The enolase superfamily: A general strategy for enzymecatalyzed abstraction of the alpha-protons of carboxylic acids, Biochemistry 35(51):16489-16501, 1996.
57. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA, Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase, Biochemistry 47(38):9944-9954, 2008.
58. Kühnel K, Luisi BF, Crystal structure of the Escherichia coli RNA degradosome component enolase, J Mol Biol 313(3):583-592, 2001.
59. Schafer SL, Barrett WC, Kallarakal AT, Mitra B, Kozarich JW, Gerlt JA, Clifton JG, Petsko GA, Kenyon GL, Mechanism of the reaction catalyzed by mandelate racemase: Structure and mechanistic properties of the D270N mutant, Biochemistry 35(18):5662-5669, 1996.
60. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, The protein data bank, Nucleic Acids Res 28(1):235-242, 2000.