A mechanistic model of the cysteine synthase complex.: Additional material for Feldman-Salit A, Wirtz M, Hell R, Wade RC. J Mol Biol. 2009 Feb 13;386(1):37-59. Epub 2008 Sep 5 .
Free energies of hydration from Thermodynamic Integration: Comparison of Molecular
Mechanics Force Fields and Evaluation of Calculation Accuracy : Additional material for Helms,V. and Wade, R.C. J. Comp. Chem. (1997) 18, 449-462.
Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using
a Set of Human Synovial Fluid Phospholipase A2 Inhibitors : Additional material
for Ortiz et al. J. Med. Chem. (1997) 40, 1136-1148, 4168.
Live library of auxin compounds : Additional material for our auxin classification study described in Tomic et al.J. Comput. Aided Des. (1998) 12, 63-79. and Tomic et al, Internet J. Chem. (1998) 1, 26.
The cisProline(i-1)-Aromatic(i) Interaction: Folding of the Ala-cisPro-Tyr peptide
characterized by NMR and theoretical approaches: Additional material for Nardi et al. J. Biomol. NMR (2000) 17, 63-77.
Blue copper proteins: a comparative analysis of their molecular interaction properties:
Additional material for De Rienzo et al. Protein Sci. (2000) 9, 1439-54.
The structures of docked CP450cam / Pdx complex.
Additional material for A. Karyakin et al. BBA (2006)
Comparative Binding Energy (COMBINE) Analysis of OppA-peptide Complexes.
Additional material for Wang & Wade J Med. Chem. (2002) 45, 4828-4837.
Movies of ligand egress from cytochromes P450 simulated by Random Expulsion Molecular Dynamics (Luedemann et al., Internet J. Chem. (2001) 4, 6.)
Movie of barnase-barstar association trajectory simulated by Brownian Dynamics
(zipped quicktime, 974k) (Gabdoulline, R.R. and Wade, R.C. Biophys. J. (1997) 72, 1917-1929.
Movie of a trajectory of superoxide diffusing up to myeloperoxidase simulated by Brownian Dynamics
(zipped quicktime, 6.1Mb) (Gabdoulline, R.R., Kummer, U., Olsen, L.F. and Wade, R.C. Biophys. J. (2003) 85, 1421-1428).
Movie of three trajectories of barnase and barstar docking simulated by molecular dynamics with
three different implicit solvent models
(mpeg, 3Mb) (Wang, T., Wade, R.C. Proteins (2003) 50, 158-169).
Movies of ligand egress from cytochrome P4502C5 simulated by Random Acceleration Molecular Dynamics (3 Movies of 2-3Mb, mpeg) (Schleinkofer et al., EMBO Reports (2005) 6, 584-589.)
Cytochrome P450 heme force field parameters
Selected Pointers for Protein Modeling