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Results: 1 to 20 of 103

1.

COPICAT: a software system for predicting interactions between proteins and chemical compounds.

Sakakibara Y, Hachiya T, Uchida M, Nagamine N, Sugawara Y, Yokota M, Nakamura M, Popendorf K, Komori T, Sato K.

Bioinformatics. 2012 Mar 1;28(5):745-6. doi: 10.1093/bioinformatics/bts031. Epub 2012 Jan 17.

PMID:
22257668
[PubMed - indexed for MEDLINE]
Free Article
2.

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
3.

Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening.

Nagamine N, Shirakawa T, Minato Y, Torii K, Kobayashi H, Imoto M, Sakakibara Y.

PLoS Comput Biol. 2009 Jun;5(6):e1000397. doi: 10.1371/journal.pcbi.1000397. Epub 2009 Jun 5.

PMID:
19503826
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

NL MIND-BEST: a web server for ligands and proteins discovery--theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum.

González-Díaz H, Prado-Prado F, Sobarzo-Sánchez E, Haddad M, Maurel Chevalley S, Valentin A, Quetin-Leclercq J, Dea-Ayuela MA, Teresa Gomez-Muños M, Munteanu CR, José Torres-Labandeira J, García-Mera X, Tapia RA, Ubeira FM.

J Theor Biol. 2011 May 7;276(1):229-49. doi: 10.1016/j.jtbi.2011.01.010. Epub 2011 Jan 26.

PMID:
21277861
[PubMed - indexed for MEDLINE]
5.

A web-based platform for virtual screening.

Watson P, Verdonk M, Hartshorn MJ.

J Mol Graph Model. 2003 Sep;22(1):71-82.

PMID:
12798392
[PubMed - indexed for MEDLINE]
6.

Kernel methods for predicting protein-protein interactions.

Ben-Hur A, Noble WS.

Bioinformatics. 2005 Jun;21 Suppl 1:i38-46.

PMID:
15961482
[PubMed - indexed for MEDLINE]
Free Article
7.

Computational identification of ubiquitylation sites from protein sequences.

Tung CW, Ho SY.

BMC Bioinformatics. 2008 Jul 15;9:310. doi: 10.1186/1471-2105-9-310.

PMID:
18625080
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Computational screening for active compounds targeting protein sequences: methodology and experimental validation.

Wang F, Liu D, Wang H, Luo C, Zheng M, Liu H, Zhu W, Luo X, Zhang J, Jiang H.

J Chem Inf Model. 2011 Nov 28;51(11):2821-8. doi: 10.1021/ci200264h. Epub 2011 Oct 11.

PMID:
21955088
[PubMed - indexed for MEDLINE]
9.

The PSIPRED protein structure prediction server.

McGuffin LJ, Bryson K, Jones DT.

Bioinformatics. 2000 Apr;16(4):404-5.

PMID:
10869041
[PubMed - indexed for MEDLINE]
Free Article
10.

Training based on ligand efficiency improves prediction of bioactivities of ligands and drug target proteins in a machine learning approach.

Sugaya N.

J Chem Inf Model. 2013 Oct 28;53(10):2525-37. doi: 10.1021/ci400240u. Epub 2013 Sep 24.

PMID:
24020509
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
22296788
[PubMed - indexed for MEDLINE]
Free Article
12.

PCI-SS: MISO dynamic nonlinear protein secondary structure prediction.

Green JR, Korenberg MJ, Aboul-Magd MO.

BMC Bioinformatics. 2009 Jul 17;10:222. doi: 10.1186/1471-2105-10-222.

PMID:
19615046
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Protein-chemical interaction prediction via kernelized sparse learning SVM.

Shi Y, Zhang X, Liao X, Lin G, Schuurmans D.

Pac Symp Biocomput. 2013:41-52.

PMID:
23424110
[PubMed - indexed for MEDLINE]
Free Article
14.

Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure.

Koes DR, Camacho CJ.

Bioinformatics. 2012 Mar 15;28(6):784-91. doi: 10.1093/bioinformatics/btr717. Epub 2011 Dec 30. Erratum in: Bioinformatics. 2012 Jul 15;28(14):1951.

PMID:
22210869
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Application of support vector machine to three-dimensional shape-based virtual screening using comprehensive three-dimensional molecular shape overlay with known inhibitors.

Sato T, Yuki H, Takaya D, Sasaki S, Tanaka A, Honma T.

J Chem Inf Model. 2012 Apr 23;52(4):1015-26. doi: 10.1021/ci200562p. Epub 2012 Mar 27.

PMID:
22424085
[PubMed - indexed for MEDLINE]
16.

High-Throughput parallel blind Virtual Screening using BINDSURF.

Sánchez-Linares I, Pérez-Sánchez H, Cecilia JM, García JM.

BMC Bioinformatics. 2012;13 Suppl 14:S13. doi: 10.1186/1471-2105-13-S14-S13. Epub 2012 Sep 7.

PMID:
23095663
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Virtual screening for lead discovery.

Tang YT, Marshall GR.

Methods Mol Biol. 2011;716:1-22. doi: 10.1007/978-1-61779-012-6_1.

PMID:
21318897
[PubMed - indexed for MEDLINE]
18.

A new protein graph model for function prediction.

Alvarez MA, Yan C.

Comput Biol Chem. 2012 Apr;37:6-10. doi: 10.1016/j.compbiolchem.2012.01.003. Epub 2012 Jan 12.

PMID:
22381922
[PubMed - indexed for MEDLINE]
19.

A new method to estimate ligand-receptor energetics.

Bock JR, Gough DA.

Mol Cell Proteomics. 2002 Nov;1(11):904-10.

PMID:
12488466
[PubMed - indexed for MEDLINE]
Free Article
20.

CREDO: a protein-ligand interaction database for drug discovery.

Schreyer A, Blundell T.

Chem Biol Drug Des. 2009 Feb;73(2):157-67. doi: 10.1111/j.1747-0285.2008.00762.x.

PMID:
19207418
[PubMed - indexed for MEDLINE]

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