The Victor C++ library for protein representation and advanced manipulation

Bioinformatics

Volumn 31, Issue 7, 2015, Pages 1138-1140

  Hirsh, Layla ^a,b   Piovesan, Damiano ^a   Giollo, Manuel ^a   Ferrari, Carlo ^a   Tosatto, Silvio C E ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b PONTIFICIA UNIVERSIDAD CATÓLICA DEL PERÚ   (Peru)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; HUMAN; LIBRARY; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; LIBRARIES, DIGITAL; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84929143784     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu773     Document Type: Article

References (27)

1. Biasini, M. et al. (2010) OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26, 2626-2628.
2. Canutescu, A.A. and Dunbrack, R.L. (2005) MollDE: a homology modeling framework you can click with. Bioinformatics, 21, 2914-2916.
3. Chandonia, J.-M. (2007) StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics, 23, 2018-2020.
4. Fontana, P. et al. (2005) The SSEA server for protein secondary structure alignment. Bioinformatics, 21, 393-395.
5. Gamma, E. et al. (1995) Design Patterns: Elements of Reusable Object-Oriented Software. Addison-Wesley, USA.
6. Giollo, M. et al. (2014) NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation. BMC Genomics, 15 (Suppl 4), S7.
7. Grünberg, R. et al. (2007) Biskit-a software platform for structural bioinformatics. Bioinformatics, 23, 769-770.
8. Guex, N. et al. (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis, 30 (Suppl 1), S162-173.
9. Hildebrandt, A. et al. (2010) BALL-biochemical algorithms library 1.3. BMC Bioinformatics, 11, 531.
10. Huang, C.C. et al. (2014) Enhancing UCSF Chimera through web services. Nucleic Acids Res., 42, W478-W484.
11. Humphrey, W. et al. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38, 27-28.
12. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
13. Khoury, G.A. et al. (2014) WeFold: a coopetition for protein structure prediction. Proteins, 82, 1850-1868.
14. Kryshtafovych, A. et al. (2014) CASP10 results compared to those of previous CASP experiments. Proteins, 82 (Suppl 2), 164-174.
15. Kulp, D.W. et al. (2012) Structural informatics, modeling, and design with an open-source molecular software Library (MSL). J. Comput. Chem., 33, 1645-1661.
16. Loriot, S. et al. (2010) ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules. Bioinformatics, 26, 1127-1128.
17. Madhusudhan, M.S. et al. (2006) Variable gap penalty for protein sequencestructure alignment. Protein Eng. Des. Sel., 19, 129-133.
18. Martin, A.J.M. et al. (2011) RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics, 27, 2003-2005.
19. Moult, J. et al. (2014) Critical assessment of methods of protein structure prediction (CASP)-round x. Proteins, 82 (Suppl 2), 1-6.
20. Saladin, A. et al. (2009) PTools: an opensource molecular docking library. BMC Struct. Biol., 9, 27.
21. Shi, Y. et al. (2013) The polarizable atomic multipole-based AMOEBA force field for proteins. J. Chem. Theory Comput., 9, 4046-4063.
22. Sunyaev, S.R. et al. (1999) PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng., 12, 387-394.
23. Tosatto, S.C.E. et al. (2002) A divide and conquer approach to fast loop modeling. Protein Eng., 15, 279-286.
24. Tosatto, S.C.E. et al. (2006) Align: a C++ class library and web server for rapid sequence alignment prototyping. Curr. Drug Discov. Technol., 3, 167-173.
25. Tosatto, S.C.E. (2005) The victor/FRST function for model quality estimation. J. Comput. Biol., 12, 1316-1327.
26. Tosatto, S.C.E. and Battistutta, R. (2007) TAP score: torsion angle propensity normalization applied to local protein structure evaluation. BMC Bioinformatics, 8, 155.
27. Wang, G. and Dunbrack, R.L. (2004) Scoring profile-to-profile sequence alignments. Protein Sci., 13, 1612-1626.