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Items: 1 to 20 of 176

1.

Prediction of functional sites by analysis of sequence and structure conservation.

Panchenko AR, Kondrashov F, Bryant S.

Protein Sci. 2004 Apr;13(4):884-92. Epub 2004 Mar 9.

3.
4.

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.

PMID:
11524371
5.

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.

Landgraf R, Xenarios I, Eisenberg D.

J Mol Biol. 2001 Apr 13;307(5):1487-502.

PMID:
11292355
6.
7.

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics. 2008 Aug 15;24(16):i105-11. doi: 10.1093/bioinformatics/btn263.

8.

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

Laurie AT, Jackson RM.

Bioinformatics. 2005 May 1;21(9):1908-16. Epub 2005 Feb 8.

PMID:
15701681
9.

An introduction to protein contact prediction.

Hamilton N, Huber T.

Methods Mol Biol. 2008;453:87-104. doi: 10.1007/978-1-60327-429-6_3.

PMID:
18712298
10.

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N.

Proteins. 2005 Feb 15;58(3):610-7.

PMID:
15614759
11.

[Computational method for prediction of protein functional sites using specificity determinants].

Kalinina OV, Rassel RB, Rakhmaninova AB, Gel'fand MS.

Mol Biol (Mosk). 2007 Jan-Feb;41(1):151-62. Russian.

PMID:
17380902
12.

Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.

Gong S, Blundell TL.

PLoS Comput Biol. 2008 Oct 3;4(10):e1000179. doi: 10.1371/journal.pcbi.1000179.

13.

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

Saini HK, Fischer D.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W499-502. Epub 2007 May 30.

15.

Protein structure prediction based on sequence similarity.

Jaroszewski L.

Methods Mol Biol. 2009;569:129-56. doi: 10.1007/978-1-59745-524-4_7.

PMID:
19623489
16.
17.

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.

Sankararaman S, Sjölander K.

Bioinformatics. 2008 Nov 1;24(21):2445-52. doi: 10.1093/bioinformatics/btn474. Epub 2008 Sep 6.

18.
19.

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.

Bennett-Lovsey RM, Herbert AD, Sternberg MJ, Kelley LA.

Proteins. 2008 Feb 15;70(3):611-25.

PMID:
17876813
20.

Evolutionary conservation in protein folding kinetics.

Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D.

J Mol Biol. 2000 Apr 28;298(2):303-12.

PMID:
10764599

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