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Development of a generalized Born model parameterization for proteins and nucleic acids
The generalized Born model proposed by Still and co-workers is parametrized specifically for proteins, peptides, and nucleic acids within the CHARMM all hydrogen and polar hydrogen force fields and the performance of these models in reproducing overall molecular solvation trends is found to be quite good.
The effects of ionic strength on protein stability: the cold shock protein family.
An electrostatic basis for the stability of thermophilic proteins
Electrostatic interactions play an important role in determining the stability of proteins at high temperatures and the interplay between electrostatic interactions and dielectric response also provides further rationalization for the enhanced stability of thermophilic proteins with respect to cold‐denaturation.
Identifying native‐like protein structures using physics‐based potentials
The utility of physics‐based force fields in identifying native‐like conformations in a variety of preconstructed structural databases is demonstrated and proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria.
Assessing search strategies for flexible docking
- M. Vieth, J. Hirst, B. Dominy, Heidi Daigler, C. Brooks
- Computer ScienceJ. Comput. Chem.
- 15 November 1998
This work assesses the efficiency of molecular dynamics, Monte Carlo, and genetic algorithms for docking five representative ligand–receptor complexes and finds that MD is most efficient in the case of the large search space, and GA outperforms the other methods in the small search space.
Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
A flexible protein-peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein, based on a Monte Carlo annealing process, which revealed a significant correlation between energy and dRMS, important for identifying native-like conformations.
Comparison of solvation‐effect methods for the simulation of peptide interactions with a hydrophobic surface
Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively‐charged peptides on the CH3‐SAM surface.
New Family of Deamination Repair Enzymes in Uracil-DNA Glycosylase Superfamily*
- Hyun-wook Lee, B. Dominy, Weiguo Cao
- Biology, ChemistryThe Journal of Biological Chemistry
- 3 June 2011
A new class of DNA repair glycosylases that exists in bacteria, archaea, and eukaryotes as family 6 is proposed and designated as the hypoxanthine-DNA glyCosylase family, demonstrating the structural evolvability that underlies substrate specificity and catalytic flexibility in the evolution of enzymatic function.
Modeling the Influence of Salt on the Hydrophobic Effect and Protein Fold Stability
A continuum solvation based model is developed that relies on a traditional Poisson-Boltzmann term to describe the polar or electro- static effects of salt, and a surface area dependent term containing a salt concentration dependent microscopic surface tension function to capture the non-polar Hofmeister effects.
Molecular recognition and binding free energy calculations in drug development.
- B. Dominy
- Biology, ChemistryCurrent pharmaceutical biotechnology
- 31 March 2008
A broad overview of computational approaches used for the prediction of biological activity and specifically binding free energy will be presented and the biological importance of molecular recognition as well as its influence on the development of pharmaceuticals is addressed.