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Items: 1 to 20 of 107

1.

Transiting the molecular potential energy surface along low energy pathways: the TRREAT algorithm.

Campañá C, Miller RE.

J Comput Chem. 2013 Nov 5;34(29):2502-13. doi: 10.1002/jcc.23408. Epub 2013 Sep 5.

PMID:
24018749
2.

Nudged-elastic band used to find reaction coordinates based on the free energy.

Bohner MU, Zeman J, Smiatek J, Arnold A, Kästner J.

J Chem Phys. 2014 Feb 21;140(7):074109. doi: 10.1063/1.4865220.

PMID:
24559340
3.

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
4.

A growing string method for determining transition states: comparison to the nudged elastic band and string methods.

Peters B, Heyden A, Bell AT, Chakraborty A.

J Chem Phys. 2004 May 1;120(17):7877-86.

PMID:
15267702
5.

Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes.

Roth CA, Dreyfus T, Robert CH, Cazals F.

J Comput Chem. 2016 Mar 30;37(8):739-52. doi: 10.1002/jcc.24256. Epub 2015 Dec 29.

PMID:
26714673
6.

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
7.
8.

Minima hopping guided path search: an efficient method for finding complex chemical reaction pathways.

Schaefer B, Mohr S, Amsler M, Goedecker S.

J Chem Phys. 2014 Jun 7;140(21):214102. doi: 10.1063/1.4878944.

PMID:
24907985
9.

A hybrid elastic band string algorithm for studies of enzymatic reactions.

Aleksandrov A, Field M.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12544-53. doi: 10.1039/c2cp40918f. Epub 2012 May 10.

PMID:
22576234
10.

Variable-cell double-ended surface walking method for fast transition state location of solid phase transitions.

Zhang XJ, Liu ZP.

J Chem Theory Comput. 2015 Oct 13;11(10):4885-94. doi: 10.1021/acs.jctc.5b00641. Epub 2015 Oct 5.

PMID:
26574276
11.

Optimizing the structures of minimum and transition state on the free energy surface.

Yang SY, Hristov I, Fleurat-Lessard P, Ziegler T.

J Phys Chem A. 2005 Jan 13;109(1):197-204.

PMID:
16839106
12.

Mode-tracking based stationary-point optimization.

Bergeler M, Herrmann C, Reiher M.

J Comput Chem. 2015 Jul 15;36(19):1429-38. doi: 10.1002/jcc.23958. Epub 2015 Jun 15.

PMID:
26073318
13.

An algorithm to find minimum free-energy paths using umbrella integration.

Bohner MU, Kästner J.

J Chem Phys. 2012 Jul 21;137(3):034105.

PMID:
22830681
14.

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

Spiwok V, Králová B, Tvaroska I.

J Mol Model. 2008 Nov;14(11):995-1002. doi: 10.1007/s00894-008-0343-7. Epub 2008 Jul 17.

PMID:
18633653
15.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

Branduardi D, Faraldo-Gómez JD.

J Chem Theory Comput. 2013 Sep 10;9(9):4140-4154.

16.

Single-ended transition state finding with the growing string method.

Zimmerman PM.

J Comput Chem. 2015 Apr 5;36(9):601-11. doi: 10.1002/jcc.23833. Epub 2015 Jan 8.

PMID:
25581279
17.

Sampling saddle points on a free energy surface.

Samanta A, Chen M, Yu TQ, Tuckerman M, E W.

J Chem Phys. 2014 Apr 28;140(16):164109. doi: 10.1063/1.4869980.

PMID:
24784255
18.

Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

Ensing B, De Vivo M, Liu Z, Moore P, Klein ML.

Acc Chem Res. 2006 Feb;39(2):73-81.

PMID:
16489726
19.

Double-Ended Surface Walking Method for Pathway Building and Transition State Location of Complex Reactions.

Zhang XJ, Shang C, Liu ZP.

J Chem Theory Comput. 2013 Dec 10;9(12):5745-53. doi: 10.1021/ct4008475. Epub 2013 Nov 22.

PMID:
26592302
20.

An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum.

Crehuet R, Thomas A, Field MJ.

J Mol Graph Model. 2005 Oct;24(2):102-10. Epub 2005 Jun 13.

PMID:
15951211
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