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WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.

BMC Genomics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2164-14-S3-S6. Epub 2013 May 28.


Improving the prediction of disease-related variants using protein three-dimensional structure.

Capriotti E, Altman RB.

BMC Bioinformatics. 2011;12 Suppl 4:S3. doi: 10.1186/1471-2105-12-S4-S3. Epub 2011 Jul 5.


ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization.

Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY.

BMC Bioinformatics. 2008 Feb 1;9:80. doi: 10.1186/1471-2105-9-80.


DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.


SVM based prediction of RNA-binding proteins using binding residues and evolutionary information.

Kumar M, Gromiha MM, Raghava GP.

J Mol Recognit. 2011 Mar-Apr;24(2):303-13. doi: 10.1002/jmr.1061.


mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines.

Wan S, Mak MW, Kung SY.

BMC Bioinformatics. 2012 Nov 6;13:290. doi: 10.1186/1471-2105-13-290.


The LabelHash server and tools for substructure-based functional annotation.

Moll M, Bryant DH, Kavraki LE.

Bioinformatics. 2011 Aug 1;27(15):2161-2. doi: 10.1093/bioinformatics/btr343. Epub 2011 Jun 8.


WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms.

Chi SM, Nam D.

Bioinformatics. 2012 Apr 1;28(7):1028-30. doi: 10.1093/bioinformatics/bts062. Epub 2012 Jan 31.


Predicting the functional effect of amino acid substitutions and indels.

Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.


PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.

Ganesan K, Parthasarathy S.

J Struct Funct Genomics. 2011 Dec;12(4):181-9. doi: 10.1007/s10969-011-9119-x. Epub 2011 Dec 3.


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.


SIFT web server: predicting effects of amino acid substitutions on proteins.

Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W452-7. doi: 10.1093/nar/gks539. Epub 2012 Jun 11.


Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers.

Barenboim M, Masso M, Vaisman II, Jamison DC.

Proteins. 2008 Jun;71(4):1930-9. doi: 10.1002/prot.21838.


Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

Uzun A, Leslin CM, Abyzov A, Ilyin V.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W384-92. Epub 2007 May 30.


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.


Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.

Wu J, Liu H, Duan X, Ding Y, Wu H, Bai Y, Sun X.

Bioinformatics. 2009 Jan 1;25(1):30-5. doi: 10.1093/bioinformatics/btn583. Epub 2008 Nov 12.


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.


Collective judgment predicts disease-associated single nucleotide variants.

Capriotti E, Altman RB, Bromberg Y.

BMC Genomics. 2013;14 Suppl 3:S2. doi: 10.1186/1471-2164-14-S3-S2. Epub 2013 May 28.


IntelliGO: a new vector-based semantic similarity measure including annotation origin.

Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD.

BMC Bioinformatics. 2010 Dec 1;11:588. doi: 10.1186/1471-2105-11-588.


DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

Mazandu GK, Mulder NJ.

BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

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