Publications citing MMTK

Ehrlich, LP, Nilges, M, and Wade, RC (2005).
The impact of protein flexibility on protein-protein docking
Proteins-structure Function and Bioinformatics 58(1):126–133.

Ernst, M, Bruckner, S, Boresch, S, and Sieghart, W (2005).
Comparative models of GABA(A) receptor extracellular and transmembrane domains: Important insights in pharmacology and function
Molecular Pharmacology 68(5):1291–1300.

Hinsen, K, Reuter, N, Navaza, J, Stokes, DL, and Lacapere, JJ (2005).
Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase
Biophysical Journal 88(2):818–827.

Hollup, SM, Salensminde, G, and Reuter, N (2005).
WEBnm@: a web application for normal mode analyses of proteins
Bmc Bioinformatics, 6.

Issack, BB and Roy, PN (2005).
Geometric constraints in semiclassical initial value representation calculations in Cartesian coordinates: Accurate reduction in zero-point energy
Journal of Chemical Physics 123(8).

Knight, W, Hill, W, and Lodmell, JS (2005).
Ribosome Builder: A software project to simulate the ribosome
Computational Biology and Chemistry 29(2):163–174.

Markvoort, AJ, Pieterse, K, Steijaert, MN, Spijker, P, and Hilbers, PA (2005).
The bilayer-vesicle transition is entropy driven
Journal of Physical Chemistry B 109(47):22649–22654.

Carrington, BJ and Mancera, RL (2004).
Comparative estimation of vibrational entropy changes in proteins through normal modes analysis
Journal of Molecular Graphics & Modelling 23(2):167–174.

Feig, M, Karanicolas, J, and Brooks, CL (2004).
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
J. Mol. Graph. Model. 22(5):377-395.

Hixson, CA, Chen, J, Huang, ZN, and Wheeler, RA (2004).
New perspectives on multiple-copy, mean-field molecular dynamics methods
J. Mol. Graph. Model. 22(5):349-357.

Kalinowski, JA, Lesyng, B, Thompson, JD, Cramer, CJ, and Truhlar, DG (2004).
Class IV charge model for the self-consistent charge density-functional tight-binding method
Journal of Physical Chemistry A 108(13):2545–2549.

Kneller, GR and Hinsen, K (2004).
Fractional Brownian dynamics in proteins
Journal of Chemical Physics 121(20):10278–10283.

Lee, SJ, Chung, HY, and Kim, KS (2004).
An easy-to-use three-dimensional molecular visualization and analysis program: POSMOL
Bulletin of the Korean Chemical Society 25(7):1061–1064.

Ming, DM and Bruschweiler, R (2004).
Prediction of methyl-side chain dynamics in proteins
Journal of Biomolecular Nmr 29(3):363–368.

Murzyn, K, Rog, T, and Pasenkiewicz-Gierula, M (2004).
Interactions of magainin-2 amide with membrane lipids
Computational Science - Iccs 2004, Pt 2, Proceedings, 3037:325–331.

Painter, J and Merritt, EA (2004).
mmLib Python toolkit for manipulating annotated structural models of biological macromolecules
J. Appl. Cryst. 37:174-178.

Schmid, R (2004).
Car-Parrinello simulations with a real space method
Journal of Computational Chemistry 25(6):799–812.

Wako, H, Kato, M, and Endo, S (2004).
ProMode: a database of normal mode analyses on protein molecules with a full-atom model
Bioinformatics 20(13):2035–2043.

Carpy, AJ and Marchand-Geneste, N (2003).
e-Molecular shapes and properties
Sar and Qsar in Environmental Research 14(5):329–337.

Hamelryck, T and Manderick, B (2003).
PDB file parser and structure class implemented in Python
Bioinformatics 19(17):2308–2310.

Murzyn, K and Pasenkiewicz-Gierula, M (2003).
Construction of a toroidal model for the magainin pore
Journal of Molecular Modeling 9(4):217–224.

Reuter, N, Hinsen, K, and Lacapere, JJ (2003).
Transconformations of the SERCA1 Ca-ATPase: A normal mode study
Biophysical Journal 85(4):2186–2197.

Reuter, N, Hinsen, K, and Lacapere, JJ (2003).
The nature of the low-frequency normal modes of the E1lCa form of the SERCA1 Ca2+-ATPase
Na,k-atpase and Related Cation Pumps, 986:344–346.

Rog, T, Murzyn, K, Hinsen, K, and Kneller, GR (2003).
nMoldyn: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations
Journal of Computational Chemistry 24(5):657–667.

Rossmeisl, J, Hinnemann, B, Jacobsen, KW, Norskov, JK, Olsen, OH, and Pedersen, JT (2003).
A simple and realistic model system for studying hydrogen bonds in beta-sheets
Journal of Chemical Physics 118(21):9783–9794.