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Curation and analysis of multitargeting agents for polypharmacological modeling.

Reddy AS, Tan Z, Zhang S.

J Chem Inf Model. 2014 Sep 22;54(9):2536-43. doi: 10.1021/ci500092j. Epub 2014 Aug 29.


The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands.

Pawson AJ, Sharman JL, Benson HE, Faccenda E, Alexander SP, Buneman OP, Davenport AP, McGrath JC, Peters JA, Southan C, Spedding M, Yu W, Harmar AJ; NC-IUPHAR.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1098-106. doi: 10.1093/nar/gkt1143. Epub 2013 Nov 14.


Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology.

Cortés-Cabrera A, Morris GM, Finn PW, Morreale A, Gago F.

Br J Pharmacol. 2013 Oct;170(3):557-67. doi: 10.1111/bph.12294.


Creation of a free, Internet-accessible database: the Multiple Target Ligand Database.

Chen C, He Y, Wu J, Zhou J.

J Cheminform. 2015 Apr 15;7:14. doi: 10.1186/s13321-015-0064-8. eCollection 2015.


Automated design of ligands to polypharmacological profiles.

Besnard J, Ruda GF, Setola V, Abecassis K, Rodriguiz RM, Huang XP, Norval S, Sassano MF, Shin AI, Webster LA, Simeons FR, Stojanovski L, Prat A, Seidah NG, Constam DB, Bickerton GR, Read KD, Wetsel WC, Gilbert IH, Roth BL, Hopkins AL.

Nature. 2012 Dec 13;492(7428):215-20. doi: 10.1038/nature11691.


The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands.

Southan C, Sharman JL, Benson HE, Faccenda E, Pawson AJ, Alexander SP, Buneman OP, Davenport AP, McGrath JC, Peters JA, Spedding M, Catterall WA, Fabbro D, Davies JA; NC-IUPHAR.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1054-68. doi: 10.1093/nar/gkv1037. Epub 2015 Oct 12.


PubChem as a source of polypharmacology.

Chen B, Wild D, Guha R.

J Chem Inf Model. 2009 Sep;49(9):2044-55. doi: 10.1021/ci9001876.


MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.


TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database.

Wang L, Ma C, Wipf P, Liu H, Su W, Xie XQ.

AAPS J. 2013 Apr;15(2):395-406. doi: 10.1208/s12248-012-9449-z. Epub 2013 Jan 5.


Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

Wiegers TC, Davis AP, Mattingly CJ.

Database (Oxford). 2014 Jun 10;2014. pii: bau050. doi: 10.1093/database/bau050. Print 2014.


Mapping drug-target interaction networks.

Tian L, Zhang S.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:2336-9. doi: 10.1109/IEMBS.2009.5335053.


EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.

Loharch S, Bhutani I, Jain K, Gupta P, Sahoo DK, Parkesh R.

Database (Oxford). 2015 Mar 16;2015. pii: bav013. doi: 10.1093/database/bav013. Print 2015.


SwissBioisostere: a database of molecular replacements for ligand design.

Wirth M, Zoete V, Michielin O, Sauer WH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1137-43. doi: 10.1093/nar/gks1059. Epub 2012 Nov 17.


Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

Chiu YY, Lin CY, Lin CT, Hsu KC, Chang LZ, Yang JM.

BMC Genomics. 2012;13 Suppl 7:S21. doi: 10.1186/1471-2164-13-S7-S21. Epub 2012 Dec 13.


PhIN: A Protein Pharmacology Interaction Network Database.

Wang Z, Li J, Dang R, Liang L, Lin J.

CPT Pharmacometrics Syst Pharmacol. 2015 Mar;4(3):e00025. doi: 10.1002/psp4.25. Epub 2015 Mar 18.


Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus.

Reker D, Rodrigues T, Schneider P, Schneider G.

Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4067-72. doi: 10.1073/pnas.1320001111. Epub 2014 Mar 3.


G4LDB: a database for discovering and studying G-quadruplex ligands.

Li Q, Xiang JF, Yang QF, Sun HX, Guan AJ, Tang YL.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1115-23. doi: 10.1093/nar/gks1101. Epub 2012 Nov 17.


Drugs Polypharmacology by In Silico Methods: New Opportunities in Drug Discovery.

Lauria A, Bonsignore R, Bartolotta R, Perricone U, Martorana A, Gentile C.

Curr Pharm Des. 2016;22(21):3073-81.


PTID: an integrated web resource and computational tool for agrochemical discovery.

Gong J, Liu X, Cao X, Diao Y, Gao D, Li H, Qian X.

Bioinformatics. 2013 Jan 15;29(2):292-4. doi: 10.1093/bioinformatics/bts651. Epub 2012 Nov 18.


Detecting drug promiscuity using Gaussian ensemble screening.

Pérez-Nueno VI, Venkatraman V, Mavridis L, Ritchie DW.

J Chem Inf Model. 2012 Aug 27;52(8):1948-61. doi: 10.1021/ci3000979. Epub 2012 Jul 19.

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