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CHARMM: The biomolecular simulation program
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. Expand
Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.
Publisher Summary This chapter discusses published analyses of protein stability based on model compound data and outlines the assumptions that have been made. The enthalpy of protein folding isExpand
MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies
The importance of computational chemistry in modern scientific research is well established. Expand
Kinetics, in silico docking, molecular dynamics, and MM‐GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP‐binding site inhibitors: The role of water
With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC50 > 50 μM), indirubin‐3′‐oxime (IC50 = 144Expand
Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.
Proton binding plays a critical role in protein structure and function. We report pK(a) calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard"Expand
Free energy simulations come of age: protein-ligand recognition.
In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecularExpand
Free energy simulations: The meaning of the individual contributions from a component analysis
A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such aExpand
Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis.
The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA)(+) rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorlyExpand
The 1.76 A resolution crystal structure of glycogen phosphorylase B complexed with glucose, and CP320626, a potential antidiabetic drug.
CP320626, a potential antidiabetic drug, inhibits glycogen phosphorylase in synergism with glucose. To elucidate the structural basis of synergistic inhibition, we determined the structure of muscleExpand