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InterEvol reference  


If you find this server useful please refer to :
Faure G, Andreani J and Guerois R. InterEvol database : Exploring the structure and evolution of protein complex interfaces. (2012) 40:D847-56. (PubMed).

Different servers and methods were used for the development of InterEvol whose references are acknowledged below :

Structures Handling


PDB

Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE.
The RCSB Protein Data Bank: redesigned web site and web services.
(2010) Nucleic Acids Res. (PubMed)

PDBsum

Laskowski RA
PDBsum new things.
(2009).  Nucleic Acids Res., 37, D355-D359. (PubMed)

PISA

Krissinel E and Henrick K.
Inference of macromolecular assemblies from crystalline state.
(2007).  J. Mol. Biol. 372, 774--797. (PubMed)

MATRAS

Kawabata T.
MATRAS: a program for protein 3D structure comparison
(2003). Nucleic Acids Res. Vol 31, 3367-9 (PubMed)

NOXclass

Hongbo Z, Domingues FS, Sommer I and Lengauer T.
NOXclass: prediction of protein-protein interaction types.
(2006). BMC Bioinformatics 2006, 7:27 (PubMed)

PyMOL

The PyMOL Molecular Graphics System, Schroedinger, LLC.

Sequences Handling


Blast, PSI-Blast

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
(1997). Nucleic Acids Res. 25:3389-3402. (PubMed)

Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF.
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
(2001).  Nucleic Acids Res. 29(14):2994-3005. (PubMed)

HHsearch suite

Soeding J.
Protein homology detection by HMM-HMM comparison.
(2005). Bioinformatics 21, 951-960. (PubMed)

Muscle

Edgar RC
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
(2004). Nucleic Acids Res. 32(5):1792-1797 (PubMed)

Uclust

Edgar RC
Search and clustering orders of magnitude faster than BLAST.
(2010). Bioinformatics 26(19):2460-1 (PubMed)

JalView

Waterhouse AM, Procter JB, Martin DMA, Clamp M and Barton GJ
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
(2009) Bioinformatics 25 (9) 1189-1191(PubMed)