Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 113

1.

Exploration of conformational transition pathways from coarse-grained simulations.

Sfriso P, Hospital A, Emperador A, Orozco M.

Bioinformatics. 2013 Aug 15;29(16):1980-6. doi: 10.1093/bioinformatics/btt324. Epub 2013 Jun 5.

PMID:
23740746
2.

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.

Sfriso P, Emperador A, Orellana L, Hospital A, Gelpí JL, Orozco M.

J Chem Theory Comput. 2012 Nov 13;8(11):4707-18. doi: 10.1021/ct300494q. Epub 2012 Sep 6.

PMID:
26605625
3.

Using robotics to fold proteins and dock ligands.

Brutlag D, Apaydin S, Guestrin C, Hsu D, Varma C, Singh A, Latombe JC.

Bioinformatics. 2002;18 Suppl 2:S74.

PMID:
12385986
4.

Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics.

Hills RD Jr.

Methods Mol Biol. 2014;1084:123-40. doi: 10.1007/978-1-62703-658-0_7.

PMID:
24061919
5.

Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.

Emperador A, Meyer T, Orozco M.

Proteins. 2010 Jan;78(1):83-94. doi: 10.1002/prot.22563.

PMID:
19816993
6.

MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

Yamamori Y, Kitao A.

J Chem Phys. 2013 Oct 14;139(14):145105. doi: 10.1063/1.4823743. Erratum in: J Chem Phys. 2013 Dec 14;139(22):229902.

PMID:
24116651
7.

Predicting large-scale conformational changes in proteins using energy-weighted normal modes.

Palmer DS, Jensen F.

Proteins. 2011 Oct;79(10):2778-93. doi: 10.1002/prot.23105. Epub 2011 Aug 22.

PMID:
21905106
8.

Multiscale investigation of chemical interference in proteins.

Samiotakis A, Homouz D, Cheung MS.

J Chem Phys. 2010 May 7;132(17):175101. doi: 10.1063/1.3404401.

PMID:
20459186
9.

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Kim DN, Altschuler J, Strong C, McGill G, Bathe M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D451-5. doi: 10.1093/nar/gkq1088. Epub 2010 Nov 3.

10.

Randomized tree construction algorithm to explore energy landscapes.

Jaillet L, Corcho FJ, Pérez JJ, Cortés J.

J Comput Chem. 2011 Dec;32(16):3464-74. doi: 10.1002/jcc.21931. Epub 2011 Sep 14.

PMID:
21919017
11.

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.

PMID:
21967761
12.

Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins.

Soheilifard R, Makarov DE, Rodin GJ.

J Chem Phys. 2011 Aug 7;135(5):054107. doi: 10.1063/1.3613678.

PMID:
21823690
13.
14.

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
15.

Metadynamics in essential coordinates: free energy simulation of conformational changes.

Spiwok V, Lipovová P, Králová B.

J Phys Chem B. 2007 Mar 29;111(12):3073-6. Epub 2007 Mar 6.

PMID:
17388445
16.

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

Krüger DM, Ahmed A, Gohlke H.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W310-6. doi: 10.1093/nar/gks478. Epub 2012 Jun 4.

17.

Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory.

de Marco G, Várnai P.

Phys Chem Chem Phys. 2009 Dec 7;11(45):10694-700. doi: 10.1039/b917109f. Epub 2009 Oct 1.

PMID:
20145813
18.

Conformational free energy modeling of druglike molecules by metadynamics in the WHIM space.

Spiwok V, Hlat-Glembová K, Tvaroška I, Králová B.

J Chem Inf Model. 2012 Mar 26;52(3):804-13. doi: 10.1021/ci200623n. Epub 2012 Mar 6.

PMID:
22360151
19.

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

Cazade PA, Berezovska G, Meuwly M.

Biochim Biophys Acta. 2015 May;1850(5):996-1005. doi: 10.1016/j.bbagen.2014.09.008. Epub 2014 Sep 16.

PMID:
25224733
20.

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

Emperador A, Sfriso P, Villarreal MA, Gelpí JL, Orozco M.

J Chem Theory Comput. 2015 Dec 8;11(12):5929-38. doi: 10.1021/acs.jctc.5b00660. Epub 2015 Nov 20.

PMID:
26597989

Supplemental Content

Support Center