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Results: 1 to 20 of 166

1.

HomPPI: a class of sequence homology based protein-protein interface prediction methods.

Xue LC, Dobbs D, Honavar V.

BMC Bioinformatics. 2011 Jun 17;12:244. doi: 10.1186/1471-2105-12-244.

PMID:
21682895
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Predicting protein-protein interface residues using local surface structural similarity.

Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V.

BMC Bioinformatics. 2012 Mar 18;13:41. doi: 10.1186/1471-2105-13-41.

PMID:
22424103
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.

Xue LC, Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V.

Proteins. 2014 Feb;82(2):250-67. doi: 10.1002/prot.24370. Epub 2013 Oct 17.

PMID:
23873600
[PubMed - in process]
Free Article
4.

3D-partner: a web server to infer interacting partners and binding models.

Chen YC, Lo YS, Hsu WC, Yang JM.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W561-7. Epub 2007 May 21.

PMID:
17517763
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Predicting DNA-binding sites of proteins from amino acid sequence.

Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V.

BMC Bioinformatics. 2006 May 19;7:262.

PMID:
16712732
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.

Walia RR, Caragea C, Lewis BA, Towfic F, Terribilini M, El-Manzalawy Y, Dobbs D, Honavar V.

BMC Bioinformatics. 2012 May 10;13:89. doi: 10.1186/1471-2105-13-89.

PMID:
22574904
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23031578
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Prediction of RNA binding sites in proteins from amino acid sequence.

Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D.

RNA. 2006 Aug;12(8):1450-62. Epub 2006 Jun 21.

PMID:
16790841
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

InterProSurf: a web server for predicting interacting sites on protein surfaces.

Negi SS, Schein CH, Oezguen N, Power TD, Braun W.

Bioinformatics. 2007 Dec 15;23(24):3397-9. Epub 2007 Oct 12.

PMID:
17933856
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PROMALS web server for accurate multiple protein sequence alignments.

Pei J, Kim BH, Tang M, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.

PMID:
17452345
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Predicting RNA-protein interactions using only sequence information.

Muppirala UK, Honavar VG, Dobbs D.

BMC Bioinformatics. 2011 Dec 22;12:489. doi: 10.1186/1471-2105-12-489.

PMID:
22192482
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Homology inference of protein-protein interactions via conserved binding sites.

Tyagi M, Thangudu RR, Zhang D, Bryant SH, Madej T, Panchenko AR.

PLoS One. 2012;7(1):e28896. doi: 10.1371/journal.pone.0028896. Epub 2012 Jan 31.

PMID:
22303436
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

PMID:
17570145
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.

Liu R, Hu J.

BMC Bioinformatics. 2011 May 26;12:207. doi: 10.1186/1471-2105-12-207.

PMID:
21612668
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

SPPS: a sequence-based method for predicting probability of protein-protein interaction partners.

Liu X, Liu B, Huang Z, Shi T, Chen Y, Zhang J.

PLoS One. 2012;7(1):e30938. doi: 10.1371/journal.pone.0030938. Epub 2012 Jan 26.

PMID:
22292078
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

SQUARE--determining reliable regions in sequence alignments.

Tress ML, GraƱa O, Valencia A.

Bioinformatics. 2004 Apr 12;20(6):974-5. Epub 2004 Feb 5.

PMID:
14764569
[PubMed - indexed for MEDLINE]
Free Article
17.

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.

Walia RR, Xue LC, Wilkins K, El-Manzalawy Y, Dobbs D, Honavar V.

PLoS One. 2014 May 20;9(5):e97725. doi: 10.1371/journal.pone.0097725. eCollection 2014.

PMID:
24846307
[PubMed - in process]
Free PMC Article
18.

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

Pei J, Grishin NV.

Bioinformatics. 2007 Apr 1;23(7):802-8. Epub 2007 Jan 31.

PMID:
17267437
[PubMed - indexed for MEDLINE]
Free Article
19.

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.

Xia JF, Zhao XM, Song J, Huang DS.

BMC Bioinformatics. 2010 Apr 8;11:174. doi: 10.1186/1471-2105-11-174.

PMID:
20377884
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

ESG: extended similarity group method for automated protein function prediction.

Chitale M, Hawkins T, Park C, Kihara D.

Bioinformatics. 2009 Jul 15;25(14):1739-45. doi: 10.1093/bioinformatics/btp309. Epub 2009 May 12.

PMID:
19435743
[PubMed - indexed for MEDLINE]
Free PMC Article

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