Molecular dynamics simulation proteins

Hansson T and J Aqvist 1995. Estimation of Binding Free Energies for HIV Proteinase Inhibitors b Molecular Dynamics Simulations. Protein Engineering 8 1137-1144. 

AG Anderson, J Hermans. Microfoldmg Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins 3 262-265, 1988. 

Colombo, G., Roccatano, D., and Mark, A. E. (2002). Folding and stability of the three-stranded beta-sheet peptide betanova Insights from molecular dynamics simulations. Proteins Strud. Fund. Genet. 46, 380—392. 

Mangoni M, Roccatano D, Di Nola A. 1999. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 35(2) 153-162. 

Hamelberg D, Mongan J, McCammon JA (2004) Enhanced sampling of conformational transitions in proteins using full atomistic accelerated molecular dynamics simulations. Protein Sci 13 76-76... 

Li C, Shen J, Li W et al (2011) Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations. Proteins 79(6) 1800-1809... 

Ferrara P, J Apostolakis, A Caflisch (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins Struct., Funct., Genet. 46 (1) 24—33... 

Wang W, Wang J, Kollman PA (1999) What determines the van der Waals coefficient 3 in die LIE (linear interaction energy) method to estimate binding free energies using molecular dynamic simulation, Proteins, 34 395 102... 

Hansson T, Aqvist J (1995) Estimation of binding free energies for HIV protease inhibitors by molecular dynamic simulations, Protein Eng, 8 1137-1144... 

Paulsen, M. D., and Omstein, R. L., 1995, Dramatic differences in the motions of the mouth of open and closed cytochrome P450 BM3 by molecular dynamics simulations. Proteins Structure, Function and Genetics 21 2379243. 

Keywords Prion protein Molecular dynamics simulation Protein dynamics Protein misfolding pH-induced misfolding Disease-related mutations... 

Langella E, Improta R, Crescenzi O, Barone V (2006) Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKa calculations and molecular dynamics simulations. Proteins Struct Funct Bioinform 64 167... 

Yoda, T, Sugita, Y, Okamoto, Y. Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical repHca-exchange molecular dynamics simulation. Proteins 2007, 66, 846-59. 

Wang, T, Wade, R. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003, 50,158-69. 

Abseher R, Schreiber H, Steinhauser O The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins Struct., Funct., Genetics 1996, 25 366-378. 

Rodrigues, J. R., Simoes, C. J. V., Silva, C. G., 8c Brito, R. M. M. (2010). Potentially amyloido-genic conformational intermediates populate the unfolding landscape of transthyretin Insights from molecular dynamics simulations. Protein Science, 19, 202. 

Aqueous Interfaces Biomembranes Modeling CHAR-MM The Energy Function and Its Parameterization Hydrophobic Effect Molecular Dynamics Studies of Lipid Bilayers Molecular Dynamics Techniques and Applications to Proteins Permeation of Lipid Membranes Molecular Dynamics Simulations Protein Force Fields. 

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