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1.  DMD: An Efficient And Versatile Simulation Method For Fine Protein Characterization 
The Journal of Physical Chemistry. B  2012;116(29):8375-8382.
Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semi-empirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics and sample near-native states in ab initio folding of proteins of ~100 residues.
doi:10.1021/jp2114576
PMCID: PMC3406226  PMID: 22280505
Conformational dynamics; structure prediction; implicit solvent; parallel event-driven simulation
2.  Light-regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP 
We developed a new system for light-induced protein dimerization in living cells using a novel photocaged analog of rapamycin (pRap) together with an engineered rapamycin binding domain (iFKBP). Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo.
doi:10.1021/ja109630v
PMCID: PMC3133816  PMID: 21162531
3.  Rigid substructure search 
Bioinformatics  2011;27(9):1327-1329.
Motivation: Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions.
Availability and Implementation: We provide this service through a web server at http://erebus.dokhlab.org.
Contact: dokh@unc.edu
doi:10.1093/bioinformatics/btr129
PMCID: PMC3138080  PMID: 21460026

Results 1-3 (3)