Protein level predictions 6 - Analysis of interatomic contacts

Chemical bonds and interactions between amino acid side chains determine the two- and three dimensional fold and detailed shape of the protein. Changes in these bond and interactions as a result of mutation effect the stability of the proteins and can therefore have an affect on disease susceptibility. Tools gathered into this subgroup evaluate these interatomic contacts.

Programs available

• CMA
• CSU
• KiNG
• MolProbity
• PROBE
• PyMOL
• RankViaContact

An extensive overview of tools predicting protein level changes can be found from the recent review article by Thusberg and Vihinen.Click here to return to the main page of protein prediction tools.

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Description of programs

CMA

website: CMA

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Reference: Sobolev et al. SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res., 2005, 33, Web Server issue, W39-43. doi:10.1093/nar/gki398

CSU

website: CSU

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Reference: Sobolev et al. Automated analysis of interatomic contacts in proteins. Bioinformatics, 1999, 15, 4, 327-332. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/4/327

KiNG

website:  KiNG

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Reference: Lovel et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation.Proteins, 2003, 50, 3, 437-450. doi:10.1002/prot.10286

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MolProbity

website: MolProbity

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Reference:

Davis et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res., 2007, 35, Web Server issue, W375-83. doi:10.1093/nar/gkm216

Davis et al. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res., 2004, 32, Web Server issue, W615-9. doi:10.1093/nar/gkh398

PROBE

website: PROBE

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Reference:

Word et al. Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci., 2000, 9, 11, 2251-2259. doi:10.1110/ps.9.11.2251

Word et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J.Mol.Biol., 1999, 285, 4, 1711-1733.doi:10.1006/jmbi.1998.2400   

PyMOL

website: PyMOL

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Reference: Delano et al. The PyMOL molecular graphics system. Palo Alto, CA:Delano Scientific 2002.

RankViaContact

website: RankViaContact

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Reference:Shen amd Vihinen. RankViaContact: ranking and visualization of amino acid contacts. Bioinformatics, 2003, 19, 16, 2161-2162. doi:10.1093/bioinformatics/btg293

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Useful databases

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Review articles

• Janita Thusberg and Mauno Vihinen. Pathogenic or Not? And If So, Then How? Studying the Effects of Missense Mutations Using Bioinformatics Methods. Hum Mutat. 2009 May;30(5):703-14: doi:10.1002/humu.20938

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Other articles

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Useful Links

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