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Items: 1 to 20 of 21


PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.

Lu M, Ma J.

J Mol Biol. 2013 Mar 25;425(6):1082-98. doi: 10.1016/j.jmb.2012.12.026. Epub 2013 Jan 16.


A New Method for Coarse-Grained Elastic Normal-Mode Analysis.

Lu M, Poon B, Ma J.

J Chem Theory Comput. 2006;2(3):464-471.


Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

Zhang Z, Pfaendtner J, Grafmüller A, Voth GA.

Biophys J. 2009 Oct 21;97(8):2327-37. doi: 10.1016/j.bpj.2009.08.007.


Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome.

Yan A, Wang Y, Kloczkowski A, Jernigan RL.

J Chem Theory Comput. 2008 Sep 20;4(10):1757-1767.


Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.

Yang Z, Bahar I, Widom M.

Biophys J. 2009 Jun 3;96(11):4438-48. doi: 10.1016/j.bpj.2009.03.016.


CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.

J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. Review.


Protein structure fitting and refinement guided by cryo-EM density.

Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A.

Structure. 2008 Feb;16(2):295-307. doi: 10.1016/j.str.2007.11.016.


Packing regularities in biological structures relate to their dynamics.

Jernigan RL, Kloczkowski A.

Methods Mol Biol. 2007;350:251-76.


Molecular dynamics: survey of methods for simulating the activity of proteins.

Adcock SA, McCammon JA.

Chem Rev. 2006 May;106(5):1589-615. Review. No abstract available.


The role of shape in determining molecular motions.

Lu M, Ma J.

Biophys J. 2005 Oct;89(4):2395-401. Epub 2005 Jul 29.


On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models.

Delarue M, Dumas P.

Proc Natl Acad Sci U S A. 2004 May 4;101(18):6957-62. Epub 2004 Apr 19.


Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs.

Boskovic J, Rivera-Calzada A, Maman JD, Chacón P, Willison KR, Pearl LH, Llorca O.

EMBO J. 2003 Nov 3;22(21):5875-82.


Simulation of F-actin filaments of several microns.

Ming D, Kong Y, Wu Y, Ma J.

Biophys J. 2003 Jul;85(1):27-35.


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