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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 (Qui, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005−3014) is parametrized specifically for proteins,Expand
The effects of ionic strength on protein stability: the cold shock protein family.
Continuum electrostatic models are used to examine in detail the mechanism of protein stabilization and destabilization due to salt near physiological concentrations. Three wild-type cold shockExpand
Identifying native‐like protein structures using physics‐based potentials
We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to identify the misfolded structures with over 90% accuracy. Expand
Assessing search strategies for flexible docking
We assess the efficiency of molecular dynamics MD, Monte Ž . Expand
An electrostatic basis for the stability of thermophilic proteins
Two factors provide key contributions to the stability of thermophilic proteins relative to their mesophilic homologues: electrostatic interactions of charged residues in the folded state and theExpand
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. The method is based on a Monte Carlo annealing process.Expand
Comparison of solvation‐effect methods for the simulation of peptide interactions with a hydrophobic surface
In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united‐atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit Solvation method (C22 with GBMV), and an all‐atom explicit solvation methods (TIP3P). Expand
New Family of Deamination Repair Enzymes in Uracil-DNA Glycosylase Superfamily*
DNA glycosylases play a major role in the repair of deaminated DNA damage. Previous investigations identified five families within the uracil-DNA glycosylase (UDG) superfamily. All enzymes within theExpand
Modeling the Influence of Salt on the Hydrophobic Effect and Protein Fold Stability
Salt influences protein stability through electrostatic mechanisms as well as through nonpolar Hofmeister effects. In the present work, a continuum solvation based model is developed to explore theExpand
Insights from xanthine and uracil DNA glycosylase activities of bacterial and human SMUG1: switching SMUG1 to UDG.
Single-strand-selective monofunctional uracil DNA glycosylase (SMUG1) belongs to Family 3 of the uracil DNA glycosylase (UDG) superfamily. Here, we report that a bacterial SMUG1 ortholog in GeobacterExpand