Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models

BMC Structural Biology

Volumn 8, Issue , 2008, Pages

  Latek, Dorota ^a   Kolinski, Andrzej ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; CASPASE 6;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTACT PREDICTION; CORRELATION COEFFICIENT; FORCE; INTERMETHOD COMPARISON; MOLECULAR MODEL; MONTE CARLO METHOD; NERVE CELL NETWORK; PREDICTION; PROTEIN FOLDING; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SIMULATION; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETICS; PROTEIN DATABASE;

ALGORITHMS; CASPASE 6; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 50849144042     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-36     Document Type: Article

References (50)

1. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Skolnick A Kolinski AR Ortiz, J Mol Biol 1997 265 2 217 241 9020984
2. Global fold determination from a small number of distance restraints. A Aszodi MJ Gradwell WR Taylor, J Mol Biol 1995 251 2 308 326 7643405
3. Protein secondary structure prediction based on position-specific scoring matrices. DT Jones, J Mol Biol 1999 292 2 195 202 10493868
4. CASP6 assessment of contact prediction. O Grana D Baker RM MacCallum J Meiler M Punta B Rost ML Tress A Valencia, Proteins 2005 61 Suppl 7 214 224 16187364
5. Prediction of Contact Maps Using Support Vector Machines. YKG Zhao, 3rd IEEE International Conference on Bioinformatics and Bioengineering (BIBE) 2003 26 33
6. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. M Nilges, J Mol Biol 1995 245 5 645 660 7844833
7. [Calculation of the tertiary structure of proteins on the basis of an analysis of the matrix contacts between amino acid residues]. SG Galaktionov MA Rodionov, Biofizika 1980 25 3 385 392 7397251
8. The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. TF Havel ID Kuntz GM Crippen, J Theor Biol 1983 104 3 359 381 6656266
9. Correlated mutations and residue contacts in proteins. U Gobel C Sander R Schneider A Valencia, Proteins 1994 18 4 309 317 8208723
10. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. S Miyazawa RL Jernigan, Macromolecules 1985 18 534 552
11. PROFcon: novel prediction of long-range contacts. M Punta B Rost, Bioinformatics 2005 21 13 2960 2968 15890748
12. Contact maps. A Kolinski A Godzik J Skolnick, Encyclopedia of Molecular Biology John Wiley & Sons, Creighton T, 1 1999 567 571
13. Protein Structure Prediction in 1D, 2D, and 3D. B Rost, The Encyclopaedia of Computational Chemistry 1998 3 2242 2255
14. Prediction of contact maps with neural networks and correlated mutations. P Fariselli O Olmea A Valencia R Casadio, Protein Eng 2001 14 11 835 843 11742102
15. Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. I Halperin H Wolfson R Nussinov, Proteins 2006 63 4 832 845 16508975
16. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. D Bau AJ Martin C Mooney A Vullo I Walsh G Pollastri, BMC Bioinformatics 2006 7 402 16953874
17. Predicting interresidue contacts using templates and pathways. Y Shao C Bystroff, Proteins 2003 53 Suppl 6 497 502 14579339
18. Improved residue contact prediction using support vector machines and a large feature set. J Cheng P Baldi, BMC Bioinformatics 2007 8 113 17407573
19. Striped sheets and protein contact prediction. RM MacCallum, Bioinformatics 2004 20 Suppl 1 I224 I231 15262803
20. Comparative protein structure modeling of genes and genomes. MA Marti-Renom AC Stuart A Fiser R Sanchez F Melo A Sali, Annu Rev Biophys Biomol Struct 2000 29 291 325 10940251
21. Fold recognition methods. A Godzik, Methods Biochem Anal 2003 44 525 546 12647403
22. 3D-Jury: a simple approach to improve protein structure predictions. K Ginalski A Elofsson D Fischer L Rychlewski, Bioinformatics 2003 19 8 1015 1018 12761065
23. Critical assessment of methods of protein structure prediction (CASP) - round 6. J Moult K Fidelis B Rost T Hubbard A Tramontano, Proteins 2005 61 Suppl 7 3 7 16187341
24. In silico two-hybrid system for the selection of physically interacting protein pairs. F Pazos A Valencia, Proteins 2002 47 2 219 227 11933068
25. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. AM Lesk L Lo Conte TJ Hubbard, Proteins 2001 Suppl 5 98 118 11835487
26. Ab initio Protein Structure Prediction Using Pathway Models. XSY Yuan C Bystroff, Comparative and Functional Genomics 2003 4 4 397 401
27. Effective use of sequence correlation and conservation in fold recognition. O Olmea B Rost A Valencia, J Mol Biol 1999 293 5 1221 1239 10547297
28. Ab initio folding of proteins using restraints derived from evolutionary information. AR Ortiz A Kolinski P Rotkiewicz B Ilkowski J Skolnick, Proteins 1999 Suppl 3 177 185 10526366
29. Recovery of protein structure from contact maps. M Vendruscolo E Kussell E Domany, Fold Des 1997 2 5 295 306 9377713
30. Protein structure prediction: combining de novo modeling with sparse experimental data. D Latek D Ekonomiuk A Kolinski, J Comput Chem 2007 28 10 1668 1676 17342709
31. Assessment of intramolecular contact predictions for CASP7. JM Izarzugaza O Grana ML Tress A Valencia ND Clarke, Proteins 2007 69 Suppl 8 152 158 17671976
32. Protein modeling and structure prediction with a reduced representation. A Kolinski, Acta Biochim Pol 2004 51 2 349 371 15218533
33. Scoring docking models with evolutionary information. M Tress D de Juan O Grana MJ Gomez P Gomez-Puertas JM Gonzalez G Lopez A Valencia, Proteins 2005 60 2 275 280 15981273
34. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. A Kolinski JM Bujnicki, Proteins 2005 61 Suppl 7 84 90 16187348
35. A "FRankenstein's monster" approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. J Kosinski I Cymerman M Feder M Kurowski J Sasin J Bujnicki, Proteins 2003 53 Suppl 6 369 379 14579325
36. Protein contact prediction using patterns of correlation. N Hamilton K Burrage MA Ragan T Huber, Proteins 2004 56 4 679 684 15281121
37. Prediction of residue-residue contacts using correlated mutation and hydrophobic packing score. MK Song K Joo J Lee, CASP6 Abstract Book 2004 85
38. SAM-T04: what is new in protein-structure prediction for CASP6. K Karplus S Katzman G Shackleford M Koeva J Draper B Barnes M Soriano R Hughey, Proteins 2005 61 Suppl 7 135 142 16187355
39. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. G Pollastri P Baldi, Bioinformatics 2002 18 Suppl 1 S62 70 12169532
40. A neural network based predictor of residue contacts in proteins. P Fariselli R Casadio, Protein Eng 1999 12 1 15 21 10065706
41. Parallel Tempering Algorithm for Conformational Studies of Biological Molecules. U Hansmann, Chemical Physics Letters 1997 281 1-3 140 150
42. Protein folding with a reduced model and inaccurate short-range restraints. D Plewczynska A Kolinski, Macromol Theory Simul 2005 14 7 444 451
43. Characterization of protein-folding pathways by reduced-space modeling. S Kmiecik A Kolinski, Proc Natl Acad Sci USA 2007 104 30 12330 12335 17636132
44. Hierarchical modeling of protein interactions. M Kurcinski A Kolinski, J Mol Model 2007 13 6-7 691 698 17297609
45. The PSIPRED protein structure prediction server. LJ McGuffin K Bryson DT Jones, Bioinformatics 2000 16 4 404 405 10869041
46. HCPM - program for hierarchical clustering of protein models. D Gront A Kolinski, Bioinformatics 2005 21 14 3179 3180 15840705
47. Evaluating CASP4 predictions with physical energy functions. M Feig CL Brooks 3rd, Proteins 2002 49 2 232 245 12211003
48. Scoring function for automated assessment of protein structure template quality. Y Zhang J Skolnick, Proteins 2004 57 4 702 710 15476259
49. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. S Kmiecik D Gront A Kolinski, BMC Struct Biol 2007 7 43 17603876
50. Protein structure prediction using Rosetta. CA Rohl CE Strauss KM Misura D Baker, Methods Enzymol 2004 383 66 93 15063647