Structural bioinformatics

Structural bioinformatics is the branch of bioinformatics which is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structure such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, and binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology.

See also

References

Books

• Bourne, P.E., and Gu, J. (2009) Structural Bioinformatics (2nd edition), John Wiley & Sons, New York, ISBN 978-0-470-18105-8
• Bourne, P.E., and Weissig, H. (2003) Structural Bioinformatics, Wiley ISBN 0-471-20199-5
• Leach, Andrew (2001) Molecular Modelling: Principles and Applications (2nd edition), Prentice Hall, ISBN 978-0-582-38210-7
• Peitsch, M.C., and Schwede, T. (2008) Computational Structural Biology: Methods and Applications World Scientific, ISBN 978-9812778772

Hallmark publications

• Leontis NB, Westhof E. (2001). "Geometric nomenclature and classification of RNA base pairs". RNA 7 (4): 499–512. doi:10.1017/S1355838201002515. PMC 1370104. PMID 11345429. 
• Richardson JS. (1981). "The anatomy and taxonomy of protein structure". Adv Protein Chem. Advances in Protein Chemistry 34: 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 978-0-12-034234-1. PMID 7020376. 
• Ramachandran GN, Sasisekharan V. (1968). "Conformation of polypeptides and proteins". Adv Protein Chem. Advances in Protein Chemistry 23: 283–438. doi:10.1016/S0065-3233(08)60402-7. ISBN 978-0-12-034223-5. PMID 4882249. 
• Ramachandran GN, Ramakrishnan C, Sasisekharan V. (1963). "Stereochemistry of polypeptide chain configurations". J Mol Biol 7: 95–9. doi:10.1016/S0022-2836(63)80023-6. PMID 13990617. 

External links

Databases

• MMDB
• Protein Data Bank (PDB)
• Nucleic acid Data Base (NDB)
• Structural Classification of Proteins (SCOP)
• TOPOFIT-DB
• Electron Density Server (EDS)
• CASP Prediction Center
• PISCES server for creating non-redundant lists of proteins
• The Structural Biology Knowledgebase
• ProtCID: The Protein Common Interface Database

Software

• BALLView molecular modeling and visualization
• FRIEND visualization and analysis
• STING visualization and analysis
• PyMOL viewer and modeling
• VMD viewer, molecular dynamics
• KiNG, an open-source Java kinemage viewer
• MolMol viewer, NMR
• SPDBV DeepView viewer
• STRIDE determination of secondary structure from coordinates
• MolProbity structure-validation web server
• PROCHECK, a structure-validation web service
• CheShift, a protein structure-validation on-line application
• MolTalk, structural bioinformatics software
• Jmol, a molecular viewer Java applet with rasmol-like scripting capabilities and Javascript interaction
• [http://propka.ki.ku.dk, PROPKA], rapid prediction of protein pKa values based on empirical structure/function relationships
• CARA – Computer Aided Resonance Assignment
• Docking Server, a molecular docking web server
• StarBiochem, a java protein viewer, features direct search of protein databank
• Biskit, a python platform for structural bioinformatics
• SPADE the structural proteomics application development environment
• UGENE, an opensource multiplatform viewer for PDB and MMDB files
• PocketSuite, a web portal for various web-servers for binding site level analysis
• MSL, an open-source C++ molecular modeling software library for the implementation of structural analysis, prediction and design methods