New theoretical techniques are being developed and characterized. These efforts are usually coupled with software development, and involve the systematic testing and evaluation of new ideas. This development is driven by current needs and interests. Specific ongoing projects include: - Develop electric density map docking utility, provide a efficient tool for electric density map experimental studies. - Refine protein structure prediction exploration, Explore informational approach to predict protein structure. - Development of methods for examining reaction mechanism in complex systems. - Unbiased forced sampling of complex conformational transitions and estimation of the potential of mean force along the reaction pathway - Development of the REPLICA/PATH method for determining reaction paths in complex systems using simulated annealing - Development of combined Quantum Mechanical/Molecular Modeling (QM/MM) potentials (Gaussian delocalize MM charges, double link atom method) - GAMESS-UK and CHARMM integration for QM/MM applications - Density functional QM/MM using a double link atom interface - Evaluation of alternate treatments of QM/MM interfaces - Rational drug design: shape descriptor facility for CHARMM - Development of accurate interaction energy calculations for macromolecules - Development of a rapid search strategy for docking two macromolecules - Development of efficient and accurate solvation model using aqueous solution simulation to provide solvation force information. Quantum mechanical/molecular mechanical (QM/MM) techniques are extremely useful in the theoretical examination of competing reaction pathways in enzyme mechanisms. The laboratory has developed the 'Double link atoms with gaussian blur (DLA/DGMM)' technique. We have computed the rotational barriers, deprotonation energies and proton affinities of a series of model compounds. The results indicate that our method and implementation of partitioning a molecule into quantum and molecular mechanics regions is robust and would be extremely helpful in studying enzyme mechanisms. GAMESS-UK has been tightly integrated into CHARMM to allow studies of catalytic paths in small molecules and enzyme complexes. This extends the QM/MM suite within CHARMM since GAMESS-UK provides DFT (Density Functional Theory). Gaussian convolution (blurring) of classical partial charges has been implemented and tested. These delocalized charges reduce artifacts and improve on the double link atom methodology for treating QM/MM boundary conditions. In collaboration with Prof. Toshiko Ichiye, there is an effort to refine and further develop a new potential energy function for liquid water, which is crucial for accurate computer simulations of biological molecules in realistic environments. The water model, which is referred to as the soft sticky dipole (SSD) model, is both faster and more accurate than currently used models. Currently, the focus is on adding electronic polarizability into SSD water, which will enhance the ability to model water in specialized environments such as inside membrane pores and channels or near metal sites.
| Lee, Juyong; Lee, In-Ho; Joung, InSuk et al. (2017) Finding multiple reaction pathways via global optimization of action. Nat Commun 8:15443 |
| Lee, Juyong; Zhang, Zhong-Yuan; Lee, Jooyoung et al. (2017) Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise. Sci Rep 7:12399 |
| Huang, Jing; Simmonett, Andrew C; Pickard 4th, Frank C et al. (2017) Mapping the Drude polarizable force field onto a multipole and induced dipole model. J Chem Phys 147:161702 |
| Tao, Peng; Hodoš?ek, Milan; Larkin, Joseph D et al. (2012) Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints. J Chem Theory Comput 8:5035-5051 |
| Ghysels, A; Van Neck, D; Brooks, B R et al. (2009) Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach. J Chem Phys 130:084107 |
| Miller, Benjamin T; Zheng, Wenjun; Venable, Richard M et al. (2008) Langevin network model of myosin. J Phys Chem B 112:6274-81 |
| O'Brien, Edward P; Ziv, Guy; Haran, Gilad et al. (2008) Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A 105:13403-8 |
| Woodcock, H Lee; Brooks, Bernard R; Pastor, Richard W (2008) Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran. J Am Chem Soc 130:6345-7 |
| Miller, Benjamin T; Singh, Rishi P; Klauda, Jeffery B et al. (2008) CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model 48:1920-9 |
| Zheng, Wenjun; Brooks, Bernard R; Hummer, Gerhard (2007) Protein conformational transitions explored by mixed elastic network models. Proteins 69:43-57 |
Showing the most recent 10 out of 37 publications
