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Integrated Modeling Program, Applied Chemical Theory (IMPACT)
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanicsExpand
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Simplified amino acid alphabets for protein fold recognition and implications for folding.
Protein design experiments have shown that the use of specific subsets of amino acids can produce foldable proteins. This prompts the question of whether there is a minimal amino acid alphabet whichExpand
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AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling
We have developed an implicit solvent effective potential (AGBNP) that is suitable for molecular dynamics simulations and high‐resolution modeling. It is based on a novel implementation of theExpand
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HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new leadExpand
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Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein.
The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation uponExpand
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Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics.
Molecular dynamics simulations are employed to determine the errors introduced by anharmonicity and anisotropy in the structure and temperature factors obtained for proteins by refinement of X-rayExpand
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On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.
Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling ofExpand
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Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.
The antibacterial peptide microcin J25 (MccJ25) inhibits transcription by bacterial RNA polymerase (RNAP). Biochemical results indicate that inhibition of transcription occurs at the level of NTPExpand
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New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model
A new linear interaction energy (LIE) method based on a continuum solvent surface generalized Born (SGB) model is proposed for protein−ligand binding affinity calculations. The new method SGB-LIE isExpand
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Biliary cast syndrome following liver transplantation: Predictive factors and clinical outcomes
Biliary cast syndrome (BCS), the presence of biliary casts and debris causing biliary obstruction, occurs in 4%‐18% of orthotopic liver transplant (OLT) recipients. Potential consequences includeExpand
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