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Items: 1 to 20 of 99

1.

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL.

Bioinformatics. 2012 May 1;28(9):1278-9. doi: 10.1093/bioinformatics/bts139. Epub 2012 Mar 21.

PMID:
22437851
2.

FlexServ: an integrated tool for the analysis of protein flexibility.

Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpí JL, Orozco M.

Bioinformatics. 2009 Jul 1;25(13):1709-10. doi: 10.1093/bioinformatics/btp304. Epub 2009 May 7.

PMID:
19429600
3.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

Hospital A, Andrio P, Cugnasco C, Codo L, Becerra Y, Dans PD, Battistini F, Torres J, Goñi R, Orozco M, Gelpí JL.

Nucleic Acids Res. 2016 Jan 4;44(D1):D272-8. doi: 10.1093/nar/gkv1301. Epub 2015 Nov 26.

4.

A Grid-enabled web portal for NMR structure refinement with AMBER.

Bertini I, Case DA, Ferella L, Giachetti A, Rosato A.

Bioinformatics. 2011 Sep 1;27(17):2384-90. doi: 10.1093/bioinformatics/btr415. Epub 2011 Jul 14.

PMID:
21757462
5.

ST-analyzer: a web-based user interface for simulation trajectory analysis.

Jeong JC, Jo S, Wu EL, Qi Y, Monje-Galvan V, Yeom MS, Gorenstein L, Chen F, Klauda JB, Im W.

J Comput Chem. 2014 May 5;35(12):957-63. doi: 10.1002/jcc.23584. Epub 2014 Mar 17.

PMID:
24638223
6.

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.

van Dijk M, Wassenaar TA, Bonvin AM.

J Chem Theory Comput. 2012 Oct 9;8(10):3463-72. doi: 10.1021/ct300102d. Epub 2012 Apr 18.

PMID:
26592996
7.

ClickMD: an intuitive web-oriented molecular dynamics platform.

Cristiani A, Brisotto N, Cedrati FC, Floris M, Scapozza L, Moro S.

Future Med Chem. 2011 Jun;3(8):923-31. doi: 10.4155/fmc.11.59.

PMID:
21707396
8.

Public web-based services from the European Bioinformatics Institute.

Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R; European Bioinformatics Institute.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W3-9.

9.

GROMACS molecule & liquid database.

van der Spoel D, van Maaren PJ, Caleman C.

Bioinformatics. 2012 Mar 1;28(5):752-3. doi: 10.1093/bioinformatics/bts020. Epub 2012 Jan 11.

PMID:
22238269
10.

MOWServ: a web client for integration of bioinformatic resources.

Ramírez S, Muñoz-Mérida A, Karlsson J, García M, Pérez-Pulido AJ, Claros MG, Trelles O.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W671-6. doi: 10.1093/nar/gkq497. Epub 2010 Jun 4.

11.

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

Arnold K, Bordoli L, Kopp J, Schwede T.

Bioinformatics. 2006 Jan 15;22(2):195-201. Epub 2005 Nov 13.

PMID:
16301204
12.

NAFlex: a web server for the study of nucleic acid flexibility.

Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W47-55. doi: 10.1093/nar/gkt378. Epub 2013 May 17.

13.

iFold: a platform for interactive folding simulations of proteins.

Sharma S, Ding F, Nie H, Watson D, Unnithan A, Lopp J, Pozefsky D, Dokholyan NV.

Bioinformatics. 2006 Nov 1;22(21):2693-4. Epub 2006 Aug 29.

PMID:
16940324
14.

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.

Ghahremanpour MM, Arab SS, Aghazadeh SB, Zhang J, van der Spoel D.

Bioinformatics. 2014 Feb 1;30(3):439-41. doi: 10.1093/bioinformatics/btt680. Epub 2013 Nov 22.

PMID:
24273238
15.

WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures.

Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB.

Nucleic Acids Res. 2003 Jul 1;31(13):3324-7.

16.

iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S14. doi: 10.1186/1471-2105-10-S6-S14.

17.

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M.

Structure. 2010 Nov 10;18(11):1399-409. doi: 10.1016/j.str.2010.07.013.

18.

A World Wide Web-service to aid the development of AMBER parameters using analogy to standard parameters.

Ravna AW, Schrøder KE, Edvardsen O.

Comput Chem. 1999 Sep 1;23(5):435-7.

PMID:
10472126
19.

A practical introduction to molecular dynamics simulations: applications to homology modeling.

Nurisso A, Daina A, Walker RC.

Methods Mol Biol. 2012;857:137-73. doi: 10.1007/978-1-61779-588-6_6. Review.

PMID:
22323220
20.

jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability.

Roopra S, Knapp B, Omasits U, Schreiner W.

J Chem Inf Model. 2009 Oct;49(10):2412-7. doi: 10.1021/ci900248f.

PMID:
19852516

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