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Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17.PMID: 18190718 [PubMed - indexed for MEDLINE]Related articlesFree article

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O.

Protein Sci. 2006 Jun;15(6):1530-6. Epub 2006 May 2.PMID: 16672239 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.

Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O.

Bioinformatics. 2009 Jun 1;25(11):1426-7. Epub 2009 Mar 23.PMID: 19307237 [PubMed - indexed for MEDLINE]Related articlesFree article

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features.

Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O.

PLoS One. 2008 May 7;3(5):e2136.PMID: 18461181 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary Trace Annotation of Protein Function in the Structural Proteome.

Erdin S, Ward RM, Venner E, Lichtarge O.

J Mol Biol. 2009 Dec 23. [Epub ahead of print]PMID: 20036248 [PubMed - as supplied by publisher]Related articles

Prediction of enzyme function by combining sequence similarity and protein interactions.

Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B.

BMC Bioinformatics. 2008 May 27;9:249.PMID: 18505562 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

Chiang RA, Sali A, Babbitt PC.

PLoS Comput Biol. 2008 Aug 1;4(8):e1000142.PMID: 18670595 [PubMed - indexed for MEDLINE]Related articlesFree article

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Kundrotas PJ, Lensink MF, Alexov E.

Int J Biol Macromol. 2008 Aug 15;43(2):198-208. Epub 2008 May 21.PMID: 18572239 [PubMed - indexed for MEDLINE]Related articles

Automated discovery of 3D motifs for protein function annotation.

Polacco BJ, Babbitt PC.

Bioinformatics. 2006 Mar 15;22(6):723-30. Epub 2006 Jan 12.PMID: 16410325 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering structural motifs using a structural alphabet: application to magnesium-binding sites.

Dudev M, Lim C.

BMC Bioinformatics. 2007 Mar 28;8:106.PMID: 17389049 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic discovery of cross-family sequence features associated with protein function.

Brameier M, Haan J, Krings A, MacCallum RM.

BMC Bioinformatics. 2006 Jan 12;7:16.PMID: 16409628 [PubMed - indexed for MEDLINE]Related articlesFree article

Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.

Mooney C, Pollastri G.

Proteins. 2009 Oct;77(1):181-90.PMID: 19422056 [PubMed - indexed for MEDLINE]Related articles

Modeling protein loops with knowledge-based prediction of sequence-structure alignment.

Peng HP, Yang AS.

Bioinformatics. 2007 Nov 1;23(21):2836-42. Epub 2007 Sep 7.PMID: 17827204 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of function in protein superfamilies, from a structural perspective.

Todd AE, Orengo CA, Thornton JM.

J Mol Biol. 2001 Apr 6;307(4):1113-43.PMID: 11286560 [PubMed - indexed for MEDLINE]Related articles

Automatic generation of 3D motifs for classification of protein binding sites.

Nebel JC, Herzyk P, Gilbert DR.

BMC Bioinformatics. 2007 Aug 30;8:321.PMID: 17760982 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis and prediction of functionally important sites in proteins.

Chakrabarti S, Lanczycki CJ.

Protein Sci. 2007 Jan;16(1):4-13.PMID: 17192586 [PubMed - indexed for MEDLINE]Related articlesFree article

Ab initio and homology based prediction of protein domains by recursive neural networks.

Walsh I, Martin AJ, Mooney C, Rubagotti E, Vullo A, Pollastri G.

BMC Bioinformatics. 2009 Jun 26;10:195.PMID: 19558651 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of protein function from protein sequence and structure.

Whisstock JC, Lesk AM.

Q Rev Biophys. 2003 Aug;36(3):307-40. Review.PMID: 15029827 [PubMed - indexed for MEDLINE]Related articles

Predicting and improving the protein sequence alignment quality by support vector regression.

Lee M, Jeong CS, Kim D.

BMC Bioinformatics. 2007 Dec 3;8:471.PMID: 18053160 [PubMed - indexed for MEDLINE]Related articlesFree article

How well is enzyme function conserved as a function of pairwise sequence identity?

Tian W, Skolnick J.

J Mol Biol. 2003 Oct 31;333(4):863-82.PMID: 14568541 [PubMed - indexed for MEDLINE]Related articles