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Items: 1 to 20 of 105

1.

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.

Jubb HC, Higueruelo AP, Ochoa-MontaƱo B, Pitt WR, Ascher DB, Blundell TL.

J Mol Biol. 2017 Feb 3;429(3):365-371. doi: 10.1016/j.jmb.2016.12.004. Epub 2016 Dec 10.

2.

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

Kasahara K, Kinoshita K.

BMC Bioinformatics. 2014 Jan 14;15:12. doi: 10.1186/1471-2105-15-12.

3.

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.

Pires DE, Ascher DB.

Nucleic Acids Res. 2016 Jul 8;44(W1):W557-61. doi: 10.1093/nar/gkw390. Epub 2016 May 5.

4.
5.

The RING 2.0 web server for high quality residue interaction networks.

Piovesan D, Minervini G, Tosatto SC.

Nucleic Acids Res. 2016 Jul 8;44(W1):W367-74. doi: 10.1093/nar/gkw315. Epub 2016 May 19.

6.

PIC: Protein Interactions Calculator.

Tina KG, Bhadra R, Srinivasan N.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W473-6. Epub 2007 Jun 21.

7.

CREDO: a structural interactomics database for drug discovery.

Schreyer AM, Blundell TL.

Database (Oxford). 2013 Jul 18;2013:bat049. doi: 10.1093/database/bat049. Print 2013.

8.

PLIP: fully automated protein-ligand interaction profiler.

Salentin S, Schreiber S, Haupt VJ, Adasme MF, Schroeder M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W443-7. doi: 10.1093/nar/gkv315. Epub 2015 Apr 14.

9.

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database.

Bickerton GR, Higueruelo AP, Blundell TL.

BMC Bioinformatics. 2011 Jul 29;12:313. doi: 10.1186/1471-2105-12-313.

10.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83. Epub 2007 Apr 22.

11.

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.

12.

The PredictProtein server.

Rost B, Liu J.

Nucleic Acids Res. 2003 Jul 1;31(13):3300-4.

13.

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.

Finn RD, Marshall M, Bateman A.

Bioinformatics. 2005 Feb 1;21(3):410-2. Epub 2004 Sep 7.

PMID:
15353450
14.

SITEHOUND-web: a server for ligand binding site identification in protein structures.

Hernandez M, Ghersi D, Sanchez R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W413-6. doi: 10.1093/nar/gkp281. Epub 2009 Apr 26.

15.

HORI: a web server to compute Higher Order Residue Interactions in protein structures.

Sundaramurthy P, Shameer K, Sreenivasan R, Gakkhar S, Sowdhamini R.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S24. doi: 10.1186/1471-2105-11-S1-S24.

16.

VADAR: a web server for quantitative evaluation of protein structure quality.

Willard L, Ranjan A, Zhang H, Monzavi H, Boyko RF, Sykes BD, Wishart DS.

Nucleic Acids Res. 2003 Jul 1;31(13):3316-9.

17.

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.

Davis IW, Murray LW, Richardson JS, Richardson DC.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W615-9.

18.

STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Neshich G, Togawa RC, Mancini AL, Kuser PR, Yamagishi ME, Pappas G Jr, Torres WV, Fonseca e Campos T, Ferreira LL, Luna FM, Oliveira AG, Miura RT, Inoue MK, Horita LG, de Souza DF, Dominiquini F, Alvaro A, Lima CS, Ogawa FO, Gomes GB, Palandrani JF, dos Santos GF, de Freitas EM, Mattiuz AR, Costa IC, de Almeida CL, Souza S, Baudet C, Higa RH.

Nucleic Acids Res. 2003 Jul 1;31(13):3386-92.

19.

iMolTalk: an interactive, internet-based protein structure analysis server.

Diemand AV, Scheib H.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W512-6.

20.

Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions.

Brylinski M.

Chem Biol Drug Des. 2018 Feb;91(2):380-390. doi: 10.1111/cbdd.13084. Epub 2017 Aug 31.

PMID:
28816025

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