(PS)2: Protein structure prediction server version 3.0

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W338-W342

  Huang, Tsun Tsao ^a   Hwang, Jenn Kang ^a,b   Chen, Chu Huang ^c,d,e,f   Chu, Chih Sheng ^d   Lee, Chi Wen ^a   Chen, Chih Chieh ^d,g,h  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b ASIA UNIVERSITY   (Taiwan)

^c TEXAS HEART INSTITUTE   (United States)

^d KAOHSIUNG MEDICAL UNIVERSITY HOSPITAL   (Taiwan)

^e CHINA MEDICAL UNIVERSITY HOSPITAL   (Taiwan)

^f BAYLOR COLLEGE OF MEDICINE   (United States)

^g KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^h NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE RACEMASE; MULTIPROTEIN COMPLEX;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS; BACILLUS PSYCHROSACCHAROLYTICUS; CONTROLLED STUDY; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; RACEMIZATION; WEB BROWSER; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; INTERNET; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

INTERNET; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84979866840     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv454     Document Type: Article

References (29)

1. Chen, C.C., Hwang, J.K. and Yang, J.M. (2006) (PS)2: protein structure prediction server. Nucleic Acids Res., 34, W152-W157.
2. Chen, C.C., Hwang, J.K. and Yang, J.M. (2009) (PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics, 10, 366.
3. Weber, S., Thiele, H., Mir, S., Toliat, M.R., Sozeri, B., Reutter, H., Draaken, M., Ludwig, M., Altmuller, J., Frommolt, P. et al. (2011) Muscarinic acetylcholine receptor M3 mutation causes urinary bladder disease and a prune-belly-like syndrome. Am. J. Hum. Genet., 89, 668-674.
4. Soltys, D.T., Rocha, C.R., Lerner, L.K., de Souza, T.A., Munford, V., Cabral, F., Nardo, T., Stefanini, M., Sarasin, A., Cabral-Neto, J.B. et al. (2013) Novel XPG (ERCC5) mutations affect DNA repair and cell survival after ultraviolet but not oxidative stress. Hum. Mutat., 34, 481-489.
5. Kuo, Y.C., Lin, Y.H., Chen, H.I., Wang, Y.Y., Chiou, Y.W., Lin, H.H., Pan, H.A., Wu, C.M., Su, S.M., Hsu, C.C. et al. (2012) SEPT12 mutations cause male infertility with defective sperm annulus. Hum. Mutat., 33, 710-719.
6. Friedman, R., Boye, K. and Flatmark, K. (2013) Molecular modelling and simulations in cancer research. Biochim. Biophys. Acta, 1836, 1-14.
7. Huang, S.W., Hsu, Y.W., Smith, D.J., Kiang, D., Tsai, H.P., Lin, K.H., Wang, S.M., Liu, C.C., Su, I.J. and Wang, J.R. (2009) Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008. J. Clin. Microbiol., 47, 3653-3662.
8. Mosca, R., Ceol, A. and Aloy, P. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
9. Mukherjee, S. and Zhang, Y. (2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure, 19, 955-966.
10. Guerler, A., Govindarajoo, B. and Zhang, Y. (2013) Mapping monomeric threading to protein-protein structure prediction. J. Chem. Inf. Model., 53, 717-725.
11. Szilagyi, A. and Zhang, Y. (2014) Template-based structure modeling of protein-protein interactions. Curr. Opin. Struct. Biol., 24, 10-23.
12. Lu, L., Lu, H. and Skolnick, J. (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins, 49, 350-364.
13. Baspinar, A., Cukuroglu, E., Nussinov, R., Keskin, O. and Gursoy, A. (2014) PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Res., 42, W285-W289.
14. Kundrotas, P.J., Lensink, M.F. and Alexov, E. (2008) Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. Int. J. Biol. Macromol., 43, 198-208.
15. Fukuhara, N. and Kawabata, T. (2008) HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Nucleic Acids Res., 36, W185-W189.
16. Chang, C.M., Huang, Y.W., Shih, C.H. and Hwang, J.K. (2013) On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins, 81, 1192-1199.
17. Franzosa, E.A. and Xia, Y. (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol. Biol. Evol., 26, 2387-2395.
18. Yeh, S.W., Liu, J.W., Yu, S.H., Shih, C.H., Hwang, J.K. and Echave, J. (2014) Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol. Biol. Evol., 31, 135-139.
19. Liao, H., Yeh, W., Chiang, D., Jernigan, R.L. and Lustig, B. (2005) Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Eng. Des. Sel., 18, 59-64.
20. Shih, C.H., Chang, C.M., Lin, Y.S., Lo, W.C. and Hwang, J.K. (2012) Evolutionary information hidden in a single protein structure. Proteins, 80, 1647-1657.
21. Huang, T.T., del Valle Marcos, M.L., Hwang, J.K. and Echave, J. (2014) A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol. Biol., 14, 78.
22. Lin, C.P., Huang, S.W., Lai, Y.L., Yen, S.C., Shih, C.H., Lu, C.H., Huang, C.C. and Hwang, J.K. (2008) Deriving protein dynamical properties from weighted protein contact number. Proteins, 72, 929-935.
23. Goldenberg, O., Erez, E., Nimrod, G. and Ben-Tal, N. (2009) The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res., 37, D323-D327.
24. Ashkenazy, H., Erez, E., Martz, E., Pupko, T. and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
25. Yeh, S.W., Huang, T.T., Liu, J.W., Yu, S.H., Shih, C.H., Hwang, J.K. and Echave, J. (2014) Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. Biomed. Res. Int., 2014, 572409.
26. Webb, B. and Sali, A. (2014) Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics, 47, 5.6.1-5.6.32.
27. Wada, H. and Snell, E.E. (1961) The enzymatic oxidation of pyridoxine and pyridoxamine phosphates. J. Biol. Chem., 236, 2089-2095.
28. Inagaki, K., Tanizawa, K., Badet, B., Walsh, C.T., Tanaka, H. and Soda, K. (1986) Thermostable alanine racemase from Bacillus stearothermophilus: molecular cloning of the gene, enzyme purification, and characterization. Biochemistry, 25, 3268-3274.
29. Stamper, G.F., Morollo, A.A. and Ringe, D. (1998) Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine. Biochemistry, 37, 10438-10445.