Structural bioinformatics, bioinformatyka, artykuly

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//-->Structural bioinformatics1Structural bioinformaticsStructural bioinformaticsis the branch of bioinformatics which is related to the analysis and prediction of thethree-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals withgeneralizations about macromolecular 3D structure such as comparisons of overall folds and local motifs, principlesof molecular folding, evolution, and binding interactions, and structure/function relationships, working both fromexperimentally solved structures and from computational models. The termstructuralhas the same meaning as instructural biology, and structural bioinformatics can be seen as a part of computational structural biology.ReferencesBooks• Bourne, P.E., and Gu, J. (2009)Structural Bioinformatics(2nd edition), John Wiley & Sons, New York, ISBN978-0-470-18105-8• 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, ISBN978-0-582-38210-7Hallmark publications• Leontis NB, Westhof E. (2001). "Geometric nomenclature and classification of RNA base pairs".RNA7(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 inProtein Chemistry34:167–339. 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 Chemistry23:283–438. 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 chainconfigurations".J Mol Biol7:95–9. doi:10.1016/S0022-2836(63)80023-6[9]. PMID 13990617[10].External linksDatabases••••••••••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 bioinformatics2Software• 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••••SPADE[38]the structural proteomics application development environmentUGENE, an opensource multiplatform viewer for PDB and MMDB filesPocketSuite[39], a web portal for various web-servers for binding site level analysisMSL[40], an open-source C++ molecular modeling software library for the implementation of structural analysis,prediction and design methodsReferences[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. org3Article Sources and Contributors4Article Sources and ContributorsStructural bioinformaticsFree2city, 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 editsLicenseCreative Commons Attribution-Share Alike 3.0//creativecommons.org/licenses/by-sa/3.0/ [ Pobierz całość w formacie PDF ]