TAP score: Torsion angle propensity normalization applied to local protein structure evaluation

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Tosatto, Silvio C E ^a   Battistutta, Roberto ^b  

^a UNIVERSITY OF PADOVA   (Italy)

^b VENETIAN INSTITUTE OF MOLECULAR MEDICINE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY NORMALIZATION; LOCAL PROTEIN STRUCTURES; LOCAL SEQUENCES; PROTEIN MODELING; PROTEIN STRUCTURES; QUALITY PARAMETERS; REFINED MODEL; STRUCTURE DETERMINATION;

TORSIONAL STRESS;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; INTERMETHOD COMPARISON; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN STRUCTURE; SCORING SYSTEM; STRUCTURAL PROTEOMICS; TORSION ANGLE PROPENSITY SCORE; VALIDITY; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; GENETICS; METHODOLOGY; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; TORSION;

PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; TORSION;

EID: 34249778085     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-155     Document Type: Article

References (45)

1. Deshpande N Addess KJ Bluhm WF Merino-Ott JC Townsend-Merino W Zhang Q Knezevich C Xie L Chen L Feng ZK Green RK Flippen-Anderson JL Westbrook J Berman HM Bourne PE The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema Nucleic Acids Research 2005 33 D233-D237 540011 15608185 10.1093/nar/gki057
2. Kleywegt GJ Validation of protein crystal structures Acta Crystallogr D 2000 56 249-265 10.1107/S0907444999016364 10713511
3. Branden CI Jones TA Between Objectivity and Subjectivity Nature 1990 343 6260 687-689 10.1038/343687a0
4. Wilson MA Brunger AT The 1.0 angstrom crystal structure of Ca2+-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity J Mol Biol J Mol Biol 2000 301 5 1237-1256
5. Brunger AT Free R-Value - a Novel Statistical Quantity for Assessing the Accuracy of Crystal-Structures Nature 1992 355 6359 472-475 10.1038/ 355472a0
6. Kleywegt GJ Jones TA Homo crystallographicus-quo vadis? Structure 2002 10 4 465-472 10.1016/S0969-2126(02)00743-8 11937051
7. Luzzati V Traitement statistique des erreurs dans la determination des structures cristallines Acta Crystallogr 1952 5 802-810 10.1107/ S0365110X52002161
8. Read RJ Structure-Factor Probabilities for Related Structures Acta Crystallogr A 1990 46 900-912 10.1107/S0108767390005529
9. Cruickshank DW Remarks about protein structure precision Acta Crystallogr D Biol Crystallogr 1999 55 (Pt 3) 583-601 10.1107/ S0907444998012645
10. Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network J Mol Biol 1998 276 2 417-436 10.1006/jmbi.1997.1526 9512713
11. Laskowski RA MacArthur MW Thornton JM Validation of protein models derived from experiment Curr Opin Struct Biol 1998 8 5 631-639 10.1016/ S0959-440X(98)80156-5 9818269
12. Luthy R Bowie JU Eisenberg D Assessment of protein models with three-dimensional profiles Nature 1992 356 6364 83-85 10.1038/356083a0 1538787
13. Sippl MJ Recognition of errors in three-dimensional structures of proteins Proteins 1993 17 4 355-362 10.1002/prot.340170404 8108378
14. Colovos C Yeates TO Verification of protein structures: Patterns of nonbonded atomic interactions Protein Sci 1993 2 9 1511-1519 8401235
15. Melo F Feytmans E Assessing protein structures with a non-local atomic interaction energy J Mol Biol 1998 277 5 1141-1152 10.1006/ jmbi.1998.1665 9571028
16. Hooft RW Vriend G Sander C Abola EE Errors in protein structures Nature 1996 381 6580 272 10.1038/381272a0 8692262
17. Ramachandran GN Ramakrishnan C Sasisekharan V Stereochemistry of polypeptide chain. configurations J Mol Biol 1963 7 95-99 13990617
18. Kleywegt GJ Jones TA Phi/psi-chology: Ramachandran revisited Structure 1996 4 12 1395-1400 10.1016/S0969-2126(96)00147-5 8994966
19. Laskowski R MacArthur MW Moss D Thornton J Procheck: A program to check the stereochemical quality of protein structures J Appl Cryst 1993 26 283-291 10.1107/S0021889892009944
20. Hooft RW Sander C Vriend G Objectively judging the quality of a protein structure from a Ramachandran plot Comput Appl Biosci 1997 13 4 425-430 9283757
21. Oldfield TJ SQUID: A program for the analysis and display of data from crystallography and molecular dynamics J Mol Graph 1992 10 4 247-252 10.1016/0263-7855(92)80077-Q 1476999
22. Sims GE Kim SH A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring Proc Natl Acad Sci U S A 2006 103 12 4428-4432 1401231 16537409 10.1073/pnas.0511333103
23. Tosatto SC The Victor/FRST Function for Model Quality Estimation J Comput Biol 2005 12 10 1316-1327 10.1089/cmb.2005.12.1316 16379537
24. Albiero A Tosatto SC Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures Curr Drug Discov Technol 2006 3 1 75-81 10.2174/157016306776637591 16712465
25. Esposito L De Simone A Zagari A Vitagliano L Correlation between omega and psi dihedral angles in protein structures J Mol Biol 2005 347 3 483-487 10.1016/j.jmb.2005.01.065 15755444
26. Bower MJ Cohen FE Dunbrack RL Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool J Mol Biol 1997 267 5 1268-1282 10.1006/jmbi.1997.0926 9150411
27. Dunbrack RL Jr. Rotamer libraries in the 21st century Curr Opin Struct Biol 2002 12 4 431-440 10.1016/S0959-440X(02)00344-5 12163064
28. Shapovalov MV Dunbrack RL Jr. Statistical and conformational analysis of the electron density of protein side chains Proteins 2007 66 2 279-303 10.1002/prot.21150 17080462
29. Pearlman DA Case DA Caldwell JW Ross WS Cheatham TE Debolt S Ferguson D Seibel G Kollman P Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules Comput Phys Commun 1995 91 1-3 1-41 10.1016/ 0010-4655(95)00041-D
30. MacKerell AD Bashford D Bellott M Dunbrack RL Evanseck JD Field MJ Fischer S Gao J Guo H Ha S Joseph-McCarthy D Kuchnir L Kuczera K Lau FTK Mattos C Michnick S Ngo T Nguyen DT Prodhom B Reiher WE Roux B Schlenkrich M Smith JC Stote R Straub J Watanabe M Wiorkiewicz-Kuczera J Yin D Karplus M All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B J Phys Chem B 1998 102 18 3586-3616
31. Chikenji G Fujitsuka Y Takada S A reversible fragment assembly method for de novo protein structure prediction J Chem Phys J Chem Phys 2003 119 13 6895-6903
32. Jones DT McGuffin LJ Assembling novel protein folds from super-secondary structural fragments Proteins 2003 53 Suppl 6 480-485 10.1002/prot.10542 14579336
33. Rohl CA Strauss CE Misura KM Baker D Protein structure prediction using Rosetta Methods Enzymol 2004 383 66-93 15063647
34. Fang Q Shortle D Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments Proteins 2003 53 Suppl 6 486-490 10.1002/prot.10541 14579337
35. Higo J Ito N Kuroda M Ono S Nakajima N Nakamura H Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations Protein Sci 2001 10 6 1160-1171 10.1110/ps.44901 11369854
36. DePristo MA de Bakker PI Lovell SC Blundell TL Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles Proteins 2003 51 1 41-55 10.1002/prot.10285 12596262
37. Tosatto SCE Bindewald E Hesser J Männer R A divide and conquer approach to fast loop modeling Protein Engineering 2002 15 4 279-286 10.1093/protein/15.4.279 11983928
38. Fiser A Do RK Sali A Modeling of loops in protein structures Protein Sci 2000 9 9 1753-1773 11045621
39. Miyazawa S Jernigan RL Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space Proteins 2003 50 1 35-43 10.1002/prot.10242 12471597
40. Sippl MJ Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures J Comput Aided Mol Des 1993 7 4 473-501 10.1007/BF02337562 8229096
41. Shortle D Composites of local structure propensities: Evidence for local encoding of long-range structure Protein Sci 2002 11 1 18-26 10.1110/ ps.ps.31002 11742118
42. Lovell SC Davis IW Arendall WB de Bakker PI Word JM Prisant MG Richardson JS Richardson DC Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 2003 50 3 437-450 10.1002/ prot.10286 12557186
43. Chandonia JM Hon G Walker NS Lo Conte L Koehl P Levitt M Brenner SE The ASTRAL Compendium in 2004 Nucleic Acids Res 2004 32 Database issue D189-92 10.1093/nar/gkh034
44. Andreeva A Howorth D Brenner SE Hubbard TJ Chothia C Murzin AG SCOP database in 2004: Refinements integrate structure and sequence family data Nucleic Acids Res 2004 32 Database issue D226-9 10.1093/nar/gkh039
45. PDBFINDER2 http://swift.cmbi.ru.nl/gv/pdbfinder2/