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Items: 1 to 20 of 132

1.

Polypeptide folding on a conformational-space network: dependence of network topology on the structural discretization procedure.

Affentranger R, Daura X.

J Comput Chem. 2010 Jul 15;31(9):1889-903. doi: 10.1002/jcc.21476.

PMID:
20082384
2.

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

Sullivan DC, Lim C.

J Phys Chem B. 2006 Aug 24;110(33):16707-17.

PMID:
16913810
3.

Conformational dynamics of cytochrome c: correlation to hydrogen exchange.

García AE, Hummer G.

Proteins. 1999 Aug 1;36(2):175-91.

PMID:
10398365
4.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions.

Bhattacharyya M, Vishveshwara S.

Mol Biosyst. 2011 Jul;7(7):2320-30. doi: 10.1039/c1mb05038a.

PMID:
21617814
5.
6.

Conformation spaces of proteins.

Sullivan DC, Kuntz ID.

Proteins. 2001 Mar 1;42(4):495-511.

PMID:
11170204
7.
8.

Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.

Frickenhaus S, Kannan S, Zacharias M.

J Comput Chem. 2009 Feb;30(3):479-92. doi: 10.1002/jcc.21076.

PMID:
18680215
9.
10.

Conformational analysis in a multidimensional energy landscape: study of an arginylglutamate repeat.

Campos SR, Baptista AM.

J Phys Chem B. 2009 Dec 10;113(49):15989-6001. doi: 10.1021/jp902991u. Erratum in: J Phys Chem B. 2010 Jun 17;114(23):8032.

PMID:
19778072
11.

Collective Langevin dynamics of conformational motions in proteins.

Lange OF, Grubmüller H.

J Chem Phys. 2006 Jun 7;124(21):214903.

PMID:
16774438
12.

Convergence of replica exchange molecular dynamics.

Zhang W, Wu C, Duan Y.

J Chem Phys. 2005 Oct 15;123(15):154105.

PMID:
16252940
13.

Assessing equilibration and convergence in biomolecular simulations.

Smith LJ, Daura X, van Gunsteren WF.

Proteins. 2002 Aug 15;48(3):487-96.

PMID:
12112673
14.
15.
16.

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case.

Papaleo E, Mereghetti P, Fantucci P, Grandori R, De Gioia L.

J Mol Graph Model. 2009 Jun-Jul;27(8):889-99. doi: 10.1016/j.jmgm.2009.01.006.

PMID:
19264523
17.

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

Seibert MM, Patriksson A, Hess B, van der Spoel D.

J Mol Biol. 2005 Nov 18;354(1):173-83.

PMID:
16236315
18.

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM.

J Phys Chem B. 2011 Feb 17;115(6):1512-23. doi: 10.1021/jp1089596.

19.

Ensemble versus single-molecule protein unfolding.

Day R, Daggett V.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13445-50.

20.

The protein folding network.

Rao F, Caflisch A.

J Mol Biol. 2004 Sep 3;342(1):299-306.

PMID:
15313625
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