Protocol
Estimation of Folding Probabilities and Φ Values From Molecular Dynamics Simulations of Reversible Peptide Folding
Francesco Rao, Giovanni Settanni and Amedeo Caflisch
Methods in Molecular Biology™, 1, Volume 350, Protein Folding Protocols, Pages 225-249
Journal Article
Analyzing pathogenic mutations of C5 domain from cardiac myosin binding protein C through MD simulations
Fabio Cecconi, Carlo Guardiani and Roberto Livi
European Biophysics Journal, 2007, Volume 37, Number 5, Pages 683-691
Book Chapter
Sampling Kinetic Protein Folding Pathways using All-Atom Models
P.G. Bolhuis
Lecture Notes in Physics, 2006, Volume 703, Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1, Pages 393-433
Protocol
Replica Exchange Molecular Dynamics Method for Protein Folding Simulation
Ruhong Zhou
Methods in Molecular Biology™, 1, Volume 350, Protein Folding Protocols, Pages 205-223
Book Chapter
Application of Discrete Molecular Dynamics to Protein Folding and Aggregation
S. V. Buldyrev
Lecture Notes in Physics, 2008, Volume 752, Aspects of Physical Biology, Pages 97-131
Protocol
Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations
Hongxing Lei and Yong Duan
Methods in Molecular Biology™, 1, Volume 443, Molecular Modeling of Proteins, 5, Pages 277-295
Journal Article
The relationship between the solvent-accessible surface area of a protein and the number of native contacts in its structure
N. S. Bogatyreva and D. N. Ivankov
Molecular Biology, 2008, Volume 42, Number 6, Pages 932-938
Journal Article
Role of hydrophobic interactions and salt-bridges in β-hairpin folding
Aswin Sai Narain Seshasayee, Krishnan Raghunathan, Karthikeyan Sivaraman and Gautam Pennathur
Journal of Molecular Modeling, 2005, Volume 12, Number 2, Pages 197-204
Journal Article
Influence of protein flexibility on the electrostatic energy landscape in gramicidin A
Ben Corry and Shin-Ho Chung
European Biophysics Journal, 2005, Volume 34, Number 3, Pages 208-216
Journal Article
Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations
Meng Cui, Mihaly Mezei and Roman Osman
Journal of Computer-Aided Molecular Design, 2008, Volume 22, Number 8, Pages 553-561