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Structural bioinformatics
1
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.
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
Hallmark publications
• Leontis NB, Westhof E. (2001). "Geometric nomenclature and classification of RNA base pairs".
RNA
7
(4):
499–512. doi:10.1017/S1355838201002515
[1]
. PMC 1370104
[2]
. PMID 11345429
[3]
.
• Richardson JS. (1981). "The anatomy and taxonomy of protein structure"
[4]
.
Adv Protein Chem.
Advances in
Protein Chemistry
34:
167–339. doi:10.1016/S0065-3233(08)60520-3
[5]
. ISBN 978-0-12-034234-1.
PMID 7020376
[6]
.
• 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
[7]
. ISBN 978-0-12-034223-5.
PMID 4882249
[8]
.
• 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
[9]
. PMID 13990617
[10]
.
External links
Databases
•
•
•
•
•
•
•
•
•
•
MMDB
[11]
Protein Data Bank (PDB)
[12]
Nucleic acid Data Base (NDB)
[13]
Structural Classification of Proteins (SCOP)
[14]
TOPOFIT-DB
[15]
Electron Density Server (EDS)
[16]
CASP Prediction Center
[17]
PISCES server for creating non-redundant lists of proteins
[18]
The Structural Biology Knowledgebase
[19]
ProtCID: The Protein Common Interface Database
[20]
Structural bioinformatics
2
Software
• BALLView
[21]
molecular modeling and visualization
• FRIEND
[22]
visualization and analysis
• STING
[23]
visualization and analysis
• PyMOL
[24]
viewer and modeling
• VMD
[25]
viewer, molecular dynamics
• KiNG
[26]
, an open-source Java kinemage viewer
• MolMol
[27]
viewer, NMR
• SPDBV DeepView
[28]
viewer
• STRIDE
[29]
determination of secondary structure from coordinates
• MolProbity
[30]
structure-validation web server
• PROCHECK
[31]
, a structure-validation web service
• CheShift, a protein structure-validation on-line application
• MolTalk
[32]
, structural bioinformatics software
• Jmol
[33]
, a molecular viewer Java applet with rasmol-like scripting capabilities and Javascript interaction
• PROPKA
[34]
, rapid prediction of protein pKa values based on empirical structure/function relationships
• CARA
[35]
–
Computer Aided Resonance Assignment
• Docking Server
[36]
, a molecular docking web server
• StarBiochem
[37]
, a java protein viewer, features direct search of protein databank
• Biskit, a python platform for structural bioinformatics
•
•
•
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SPADE
[38]
the structural proteomics application development environment
UGENE, an opensource multiplatform viewer for PDB and MMDB files
PocketSuite
[39]
, a web portal for various web-servers for binding site level analysis
MSL
[40]
, an open-source C++ molecular modeling software library for the implementation of structural analysis,
prediction and design methods
References
[1] http:/ / dx. doi. org/ 10. 1017%2FS1355838201002515
[2] http:/ / www. ncbi. nlm. nih. gov/ pmc/ articles/ PMC1370104
[3] http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 11345429
[4] http:/ / kinemage. biochem. duke. edu/ teaching/ anatax/ index. html
[5] http:/ / dx. doi. org/ 10. 1016%2FS0065-3233%2808%2960520-3
[6] http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 7020376
[7] http:/ / dx. doi. org/ 10. 1016%2FS0065-3233%2808%2960402-7
[8] http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 4882249
[9] http:/ / dx. doi. org/ 10. 1016%2FS0022-2836%2863%2980023-6
[10] http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 13990617
[11] http:/ / www. ncbi. nlm. nih. gov/ Structure/ MMDB/ mmdb. shtml
[12] http:/ / www. pdb. org/
[13] http:/ / ndbserver. rutgers. edu/
[14] http:/ / scop. mrc-lmb. cam. ac. uk/ scop/
[15] http:/ / mozart. bio. neu. edu/ topofit/ index. php
[16] http:/ / eds. bmc. uu. se/ eds/
[17] http:/ / www. predictioncenter. org/
[18] http:/ / dunbrack. fccc. edu/ PISCES. php
[19] http:/ / sbkb. org
[20] http:/ / dunbrack2. fccc. edu/ protcid
[21] http:/ / www. ball-project. org/ Ballview
[22] http:/ / ilyinlab. org/ friend/
[23] http:/ / www. cbi. cnptia. embrapa. br/ SMS
[24] http:/ / www. pymol. org/
Structural bioinformatics
[25] http:/ / www. ks. uiuc. edu/ Research/ vmd/
[26] http:/ / kinemage. biochem. duke. edu/ software/
[27] http:/ / www. mol. biol. ethz. ch/ wuthrich/ software/ molmol/
[28] http:/ / www. expasy. org/ spdbv/
[29] http:/ / www. embl-heidelberg. de/ argos/ stride/ stride_info. html
[30] http:/ / molprobity. biochem. duke. edu/
[31] http:/ / www. biochem. ucl. ac. uk/ ~roman/ procheck/ procheck. html
[32] http:/ / www. moltalk. org/
[33] http:/ / www. jmol. org/
[34] http:/ / propka. ki. ku. dk,
[35] http:/ / cara. nmr. ch/
[36] http:/ / www. dockingserver. com/
[37] http:/ / web. mit. edu/ star/ biochem
[38] http:/ / www. spadeweb. org/
[39] http:/ / proline. physics. iisc. ernet. in/ pocketsuite/
[40] http:/ / msl-libraries. org
3
Article Sources and Contributors
4
Article Sources and Contributors
Structural bioinformatics
 Source: http://en.wikipedia.org/w/index.php?oldid=579749656  Contributors: Aloctavodia, Amkilpatrick, Bunnyhop11, Dcirovic, Dcrjsr, Docu, EVTarau, Estevezj,
Free2city, Graik, Jhjensen, Jonkerz, Lexor, Martin.jambon, Math-ghamhainn, Mdd4696, Mfursov, Michael Hardy, My very best wishes, Occhanikov, P99am, PDH, Ph.eyes, Rjwilmsi, S014djs,
Stemonitis, TallFreak, Wmclaughlin, Yeturukalidas, Ymichel, 12 anonymous edits
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