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MarkUs: a server to navigate sequence-structure-function space.

Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W357-61. doi: 10.1093/nar/gkr468. Epub 2011 Jun 14.


PUDGE: a flexible, interactive server for protein structure prediction.

Norel R, Petrey D, Honig B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W550-4. doi: 10.1093/nar/gkq475. Epub 2010 Jun 4.


PredUs: a web server for predicting protein interfaces using structural neighbors.

Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W283-7. doi: 10.1093/nar/gkr311. Epub 2011 May 23.


MESSA: MEta-Server for protein Sequence Analysis.

Cong Q, Grishin NV.

BMC Biol. 2012 Oct 2;10:82. doi: 10.1186/1741-7007-10-82.


3Drefine: an interactive web server for efficient protein structure refinement.

Bhattacharya D, Nowotny J, Cao R, Cheng J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W406-9. doi: 10.1093/nar/gkw336. Epub 2016 Apr 29.


mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

Léonard S, Joseph AP, Srinivasan N, Gelly JC, de Brevern AG.

J Biomol Struct Dyn. 2014 Apr;32(4):661-8. doi: 10.1080/07391102.2013.787026. Epub 2013 May 10.


SALIGN: a web server for alignment of multiple protein sequences and structures.

Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.


SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.

Liang H, Zhou W, Landweber LF.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W382-4.


WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures.

Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB.

Nucleic Acids Res. 2003 Jul 1;31(13):3324-7.


The PredictProtein server.

Rost B, Yachdav G, Liu J.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W321-6.


IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.

McGuffin LJ, Atkins JD, Salehe BR, Shuid AN, Roche DB.

Nucleic Acids Res. 2015 Jul 1;43(W1):W169-73. doi: 10.1093/nar/gkv236. Epub 2015 Mar 27.


ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences.

Kuznetsov IB.

Bioinformatics. 2008 Jul 1;24(13):1534-5. doi: 10.1093/bioinformatics/btn233. Epub 2008 May 14.


pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Binkowski TA, Freeman P, Liang J.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W555-8.


The HHpred interactive server for protein homology detection and structure prediction.

Söding J, Biegert A, Lupas AN.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8.


KB-Rank: efficient protein structure and functional annotation identification via text query.

Julfayev ES, McLaughlin RJ, Tao YP, McLaughlin WA.

J Struct Funct Genomics. 2012 Jun;13(2):101-10. doi: 10.1007/s10969-012-9125-7. Epub 2012 Jan 21.


Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.

Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D.

Protein Sci. 2007 Aug;16(8):1569-76.


FATCAT: a web server for flexible structure comparison and structure similarity searching.

Ye Y, Godzik A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W582-5.


CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

Krüger DM, Rathi PC, Pfleger C, Gohlke H.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W340-8. doi: 10.1093/nar/gkt292. Epub 2013 Apr 22.


SCRATCH: a protein structure and structural feature prediction server.

Cheng J, Randall AZ, Sweredoski MJ, Baldi P.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6.


The SuMo server: 3D search for protein functional sites.

Jambon M, Andrieu O, Combet C, Deléage G, Delfaud F, Geourjon C.

Bioinformatics. 2005 Oct 15;21(20):3929-30. Epub 2005 Sep 1.


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