Optimal contact definition for reconstruction of Contact Maps

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Duarte, Jose M ^a,b   Sathyapriya, Rajagopal ^a   Stehr, Henning ^a   Filippis, Ioannis ^a,c   Lappe, Michael ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b PAUL SCHERRER INSTITUTE   (Switzerland)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL METHODS; EXTENSIVE EXPLORATIONS; IMPORTANT FEATURES; MAXIMUM CONTACT MAP OVERLAP; PROTEIN STRUCTURE PREDICTION; RECONSTRUCTION PROCESS; STRUCTURAL ALIGNMENTS; STRUCTURE PREDICTION;

OPTIMIZATION; THREE DIMENSIONAL;

PROTEINS;

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 77952705908     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-283     Document Type: Article

References (41)

1. Phillips DC. The development of crystallographic enzymology. Biochem Soc Symp 1970, 30:11-28.
2. Nishikawa K, Ooi T, Isogai Y, Saito N. Tertiary Structure of Proteins. I. Representation and Computation of the Conformations. Journal of the Physical Society of Japan 1972, 32:1331-1337.
3. Caprara A, Carr R, Istrail S, Lancia G, Walenz B. 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. J Comput Biol 2004, 11:27-52. 10.1089/106652704773416876, 15072687.
4. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-138. 10.1006/jmbi.1993.1489, 8377180.
5. Alexandrov N, Shindyalov I. PDP: protein domain parser. Bioinformatics 2003, 19(3):429-430. 10.1093/bioinformatics/btg006, 12584135.
6. Emmert-Streib F, Mushegian A. A topological algorithm for identification of structural domains of proteins. BMC Bioinformatics 2007, 8:237. 10.1186/1471-2105-8-237, 1933582, 17608939.
7. Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins 2004, 55(3):508-518. 10.1002/prot.20008, 15103615.
8. Benkert P, Tosatto SCE, Schomburg D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins 2008, 71:261-277. 10.1002/prot.21715, 17932912.
9. Bolser DM, Filippis I, Stehr H, Duarte J, Lappe M. Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. BMC Struct Biol 2008, 8:53. 10.1186/1472-6807-8-53, 2642821, 19063740.
10. Melo F, Sánchez R, Sali A. Statistical potentials for fold assessment. Protein Sci 2002, 11(2):430-448. 10.1110/ps.25502, 2373452, 11790853.
11. Heringa J, Argos P. Side-chain clusters in protein structures and their role in protein folding. J Mol Biol 1991, 220:151-171. 10.1016/0022-2836(91)90388-M, 2067014.
12. Capriotti E, Fariselli P, Rossi I, Casadio R. A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics 2008, (9 Suppl 2):S6. 10.1186/1471-2105-9-S2-S6, 2323669, 18387208.
13. Sathyapriya R, Vijayabaskar MS, Vishveshwara S. Insights into protein-DNA interactions through structure network analysis. PLoS Comput Biol 2008, 4(9):e1000170. 10.1371/journal.pcbi.1000170, 2518215, 18773096.
14. Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics 2005, 21(13):2960-2968. 10.1093/bioinformatics/bti454, 15890748.
15. Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007, 8:113. 10.1186/1471-2105-8-113, 1852326, 17407573.
16. Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 2002, (18 Suppl 1):S62-S70.
17. Fariselli P, Casadio R. A neural network based predictor of residue contacts in proteins. Protein Eng 1999, 12:15-21. 10.1093/protein/12.1.15, 10065706.
18. Bartoli L, Capriotti E, Fariselli P, Martelli PL, Casadio R. The pros and cons of predicting protein contact maps. Methods Mol Biol 2008, 413:199-217. full_text, 18075167.
19. Blumenthal LM. Theory and Applications of Distance Geometry 1953, Oxford University Press, Oxford.
20. Crippen GHHT. Distance Geometry and Molecular Conformation 1988, John Wiley & Sons, New York.
21. Wüthrich K. Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science 1989, 243(4887):45-50. 10.1126/science.2911719, 2911719.
22. Glunt W, Hayden TL, Raydan M. Molecular conformations from distance matrices. J Comput Chem 1993, 14:114-120.
23. Wu D, Wu Z. An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data. J of Global Optimization 2007, 37(4):661-673.
24. Saitoh S, Nakai T, Nishikawa K. A geometrical constraint approach for reproducing the native backbone conformation of a protein. Proteins 1993, 15(2):191-204. 10.1002/prot.340150209, 8441754.
25. Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Fold Des 1997, 2(5):295-306. 10.1016/S1359-0278(97)00041-2, 9377713.
26. Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R. Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans Comput Biol Bioinform 2008, 5(3):357-367. 10.1109/TCBB.2008.27, 18670040.
27. Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999, (Suppl 3):22-29. 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W, 10526349.
28. Gromiha MM, Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J Mol Biol 2001, 310:27-32. 10.1006/jmbi.2001.4775, 11419934.
29. Vendruscolo M, Najmanovich R, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?. Proteins 2000, 38(2):134-148. 10.1002/(SICI)1097-0134(20000201)38:2<134::AID-PROT3>3.0.CO;2-A, 10656261.
30. Sathyapriya R, Duarte JM, Stehr H, Filippis I, Lappe M. Defining an Essence of Structure Determining Residue Contacts in Proteins. PLoS Comput Biol 2009, 5(12):e1000584. 10.1371/journal.pcbi.1000584, 2778133, 19997489.
31. Chen Y, Ding F, Dokholyan NV. Fidelity of the protein structure reconstruction from inter-residue proximity constraints. J Phys Chem B 2007, 111(25):7432-7438. 10.1021/jp068963t, 17542631.
32. Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins 2005, (61 Suppl 7):214-224.
33. Havel TF, Snow ME. A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 1991, 217:1-7. 10.1016/0022-2836(91)90603-4, 1988672.
34. Aszódi A, Taylor WR. Homology modelling by distance geometry. Fold Des 1996, 1(5):325-334. 10.1016/S1359-0278(96)00048-X, 9080179.
35. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779-815. 10.1006/jmbi.1993.1626, 8254673.
36. Vassura M, Margara L, Lena PD, Medri F, Fariselli P, Casadio R. FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics 2008, 24(10):1313-1315. 10.1093/bioinformatics/btn115, 18381401.
37. Stehr B, Duarte J, Filippis I, Rajagopal S, Syal K, Risbud S, Holm L, Lappe M. StruPPi: comparative modeling using consensus information from multiple templates and physics-based refinement. Abstracts book, 8th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction 2008, Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A.
38. Ponder JW. TINKER - Software tools for molecular design, User's Guide for Version 4.2 2004, Washington University School of Medicine.
39. Hodsdon ME, Ponder JW, Cistola DP. The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. J Mol Biol 1996, 264(3):585-602. 10.1006/jmbi.1996.0663, 8969307.
40. Kuszewski J, Nilges M, Brnger AT. Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm. J Biomol NMR 1992, 2:33-56. 10.1007/BF02192799, 1422145.
41. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.