SMOQ: A tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Cao, Renzhi ^a   Wang, Zheng ^b   Wang, Yiheng ^b   Cheng, Jianlin ^a  

^a University of Missouri   (United States)

^b UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; FORECASTING; PROTEINS; QUALITY CONTROL;

AMINO ACID SEQUENCE; AVERAGE DIFFERENCE; NATIVE STRUCTURES; PROTEIN SEQUENCES; SECONDARY STRUCTURES; SOLVENT ACCESSIBILITY; STRUCTURAL FEATURE; STRUCTURAL MODELING;

SUPPORT VECTOR MACHINES;

AMINO ACID; PROTEIN;

ARTICLE; ARTIFICIAL INTELLIGENCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SUPPORT VECTOR MACHINE;

AMINO ACIDS; ARTIFICIAL INTELLIGENCE; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; SUPPORT VECTOR MACHINES;

EID: 84899950974     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-120     Document Type: Article

References (45)

1. Jaravine V, Ibraghimov I, Orekhov V. Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 2006, 3(8):605-607. 10.1038/nmeth900, 16862134.
2. Lattman E. The state of the protein structure initiative. Protein Struct Funct Bioinformatics 2004, 54(4):611-615.
3. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001, 294(5540):93-96. 10.1126/science.1065659, 11588250.
4. Kryshtafovych A, Fidelis K, Moult J. Progress from CASP6 to CASP7. Protein Struct Funct Bioinformatics 2007, 69(S8):194-207.
5. Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction-Round VII. Protein Struct Funct Bioinformatics 2007, 69(S8):3-9.
6. Cozzetto D, Kryshtafovych A, Tramontano A. Evaluation of CASP8 model quality predictions. Protein Struct Funct Bioinformatics 2009, 77(S9):157-166.
7. McGuffin L. Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinforma 2007, 8:345.
8. McGuffin L. The ModFOLD server for the quality assessment of protein structural models. Bioinformatics 2008, 24(4):586. 10.1093/bioinformatics/btn014, 18184684.
9. McGuffin L, Roche D. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics 2010, 26(2):182-188. 10.1093/bioinformatics/btp629, 19897565.
10. Paluszewski M, Karplus K. Model quality assessment using distance constraints from alignments. Proteins 2008, 75:540-549.
11. Wallner B, Elofsson A. Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 2007, 69(8):184-193.
12. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004, 25(6):865-871. 10.1002/jcc.20011, 15011258.
13. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: A Simple Approach to Improve Protein Structure Predictions. Bioinformatics 2003, 19(8):1015-1018. 10.1093/bioinformatics/btg124, 12761065.
14. Wang Z, Eickholt J, Cheng J. APOLLO: a quality assessment service for single and multiple protein models. Bioinformatics 2011, 27(12):1715-1716. 10.1093/bioinformatics/btr268, 3106203, 21546397.
15. Archie J, Karplus K. Applying undertaker cost functions to model quality assessment. Proteins 2009, 75:550-555. 10.1002/prot.22288, 2992551, 19004017.
16. Benkert P, Tosatto S, Schomburg D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Structure, Function, and Bioinformatics 2008, 71(1):261-277.
17. Wallner B, Elofsson A. Can correct protein models be identified?. Protein Sci 2003, 12(5):1073-1086. 10.1110/ps.0236803, 2323877, 12717029.
18. Wang Z, Tegge A, Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 2008, 75:638-647.
19. Cheng J, Wang Z, Tegge AN, Eickholt J. Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 2009, 77(S9):181-184.
20. McGuffin L. Prediction of global and local model quality in CASP8 using the ModFOLD server. Protein Struct Funct Bioinformatics 2009, 77(S9):185-190.
21. Kryshtafovych A, Krysko O, Daniluk P, Dmytriv Z, Fidelis K. Protein structure prediction center in CASP8. Proteins 2009, 77(Suppl 9):000-000.
22. Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins 2009, 77(S9):167-172. 10.1002/prot.22476, 19544566.
23. Benkert P, Kunzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic Acids Res 2009, 37(suppl 2):W510. 2703985, 19429685.
24. Wang Z, Tegge AN, Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Protein Struct Funct Bioinformatics 2009, 75(3):638-647.
25. Ray A, Lindahl E, Wallner B. Improved model quality assessment using ProQ2. BMC Bioinforma 2012, 13(1):224.
26. Fasnacht M, Zhu J, Honig B. Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci 2007, 16(8):1557-1568. 10.1110/ps.072856307, 2203356, 17600147.
27. Sims GE, Kim S-H. A method for evaluating the structural quality of protein models by using higher-order φ-ψ pairs scoring. Proc Natl Acad Sci U S A 2006, 103(12):4428-4432. 10.1073/pnas.0511333103, 1401231, 16537409.
28. Luethy R, Bowie J, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356(6364):83-85. 10.1038/356083a0, 1538787.
29. Eisenberg D, Luthy R, Bowie J. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997, 277:396-404.
30. Sippl M. Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17:355-362. 10.1002/prot.340170404, 8108378.
31. Colovos C, Yeates T. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993, 2(9):1511. 10.1002/pro.5560020916, 2142462, 8401235.
32. Maiorov V, Abagyan R. Energy strain in three-dimensional protein structures. Fold Des 1998, 3(4):259-269. 10.1016/S1359-0278(98)00037-6, 9710569.
33. Benkert P, Schwede T, Tosatto SCE. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol 2009, 9:35. 10.1186/1472-6807-9-35, 2709111, 19457232.
34. Melo F, Feytmans E. Assessing protein structures with a non-local atomic interaction energy1. J Mol Biol 1998, 277(5):1141-1152. 10.1006/jmbi.1998.1665, 9571028.
35. Bowie J, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253(5016):164-170. 10.1126/science.1853201, 1853201.
36. Wallner B, Elofsson A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 2006, 15(4):900-913. 10.1110/ps.051799606, 2242478, 16522791.
37. Zemla A, Venclovas C, Fidelis K, Rost B. A modified definition of Sov, a segment based measure for protein secondary structure prediction assessment. Protein Struct Funct Bioinformatics 1999, 34(2):220-223.
38. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
39. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005, 33(Web Server Issue):W72-W76. 1160157, 15980571.
40. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637. 10.1002/bip.360221211, 6667333.
41. Tegge AN, Wang Z, Eickholt J, Cheng J. NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 2009, 37(suppl 2):W515. 2703959, 19420062.
42. Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci 1998, 95(11):5913-5920. 10.1073/pnas.95.11.5913, 34495, 9600892.
43. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Protein Struct Funct Bioinformatics 2004, 57(4):702-710.
44. Kryshtafovych A, Fidelis K, Tramontano A. Evaluation of model quality predictions in CASP9. Protein Struct Funct Bioinformatics 2011, 79(S10):91-106.
45. Wang Z, Eickholt J, Cheng J. MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 2010, 26(7):882-888. 10.1093/bioinformatics/btq058, 2844995, 20150411.