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Items: 1 to 20 of 116

1.

eSBMTools 1.0: enhanced native structure-based modeling tools.

Lutz B, Sinner C, Heuermann G, Verma A, Schug A.

Bioinformatics. 2013 Nov 1;29(21):2795-6. doi: 10.1093/bioinformatics/btt478. Epub 2013 Sep 9.

2.

Native structure-based modeling and simulation of biomolecular systems per mouse click.

Lutz B, Sinner C, Bozic S, Kondov I, Schug A.

BMC Bioinformatics. 2014 Aug 29;15:292. doi: 10.1186/1471-2105-15-292.

3.

SMOG@ctbp: simplified deployment of structure-based models in GROMACS.

Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W657-61. doi: 10.1093/nar/gkq498. Epub 2010 Jun 4.

4.

ALMOST: an all atom molecular simulation toolkit for protein structure determination.

Fu B, Sahakyan AB, Camilloni C, Tartaglia GG, Paci E, Caflisch A, Vendruscolo M, Cavalli A.

J Comput Chem. 2014 May 30;35(14):1101-5. doi: 10.1002/jcc.23588. Epub 2014 Mar 27.

PMID:
24676684
5.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E.

Bioinformatics. 2013 Apr 1;29(7):845-54. doi: 10.1093/bioinformatics/btt055. Epub 2013 Feb 13.

6.

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.

7.

Predicting folding free energy changes upon single point mutations.

Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E.

Bioinformatics. 2012 Mar 1;28(5):664-71. doi: 10.1093/bioinformatics/bts005. Epub 2012 Jan 11.

8.

Analyzing the effect of homogeneous frustration in protein folding.

Contessoto VG, Lima DT, Oliveira RJ, Bruni AT, Chahine J, Leite VB.

Proteins. 2013 Oct;81(10):1727-37. doi: 10.1002/prot.24309. Epub 2013 Jul 22.

PMID:
23609962
9.

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.

10.

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

Noel JK, Whitford PC, Onuchic JN.

J Phys Chem B. 2012 Jul 26;116(29):8692-702. doi: 10.1021/jp300852d. Epub 2012 May 11.

11.

MEMBPLUGIN: studying membrane complexity in VMD.

Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J.

Bioinformatics. 2014 May 15;30(10):1478-80. doi: 10.1093/bioinformatics/btu037. Epub 2014 Jan 21.

12.

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.

Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X.

Bioinformatics. 2011 Dec 1;27(23):3276-85. doi: 10.1093/bioinformatics/btr550. Epub 2011 Oct 3.

13.

Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL.

Makarewicz T, Kaźmierkiewicz R.

J Chem Inf Model. 2013 May 24;53(5):1229-34. doi: 10.1021/ci400071x. Epub 2013 May 6.

PMID:
23611462
14.

T-Pile--a package for thermodynamic calculations for biomolecules.

Gront D, Kolinski A.

Bioinformatics. 2007 Jul 15;23(14):1840-2. Epub 2007 May 17.

15.

Folding RNA/DNA hybrid duplexes.

Lorenz R, Hofacker IL, Bernhart SH.

Bioinformatics. 2012 Oct 1;28(19):2530-1. Epub 2012 Jul 24.

16.

Gro2mat: a package to efficiently read gromacs output in MATLAB.

Dien H, Deane CM, Knapp B.

J Comput Chem. 2014 Jul 30;35(20):1528-31. doi: 10.1002/jcc.23650. Epub 2014 Jun 12.

PMID:
24920464
17.

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.

18.

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

Periole X, Allen LR, Tamiola K, Mark AE, Paci E.

J Comput Chem. 2009 May;30(7):1059-68. doi: 10.1002/jcc.21128.

PMID:
18942730
19.

Combining optimal control theory and molecular dynamics for protein folding.

Arkun Y, Gur M.

PLoS One. 2012;7(1):e29628. doi: 10.1371/journal.pone.0029628. Epub 2012 Jan 6.

20.

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.

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