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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. It has been developed over the last three decades with a primary focus on… 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 is… Expand
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
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 = 144… Expand
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 a… Expand
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
- G. Archontis, T. Simonson, M. Karplus
- Chemistry, Medicine
- Journal of molecular biology
- 16 February 2001
Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been… Expand
Free Energy Simulations Come of Age: Protein—Ligand Recognition
Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis.
- J. van Heemst, Diahann T. S. L. Jansen, +14 authors R. Toes
- Medicine, Biology
- Nature communications
- 5 May 2015
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 poorly… Expand
The 1.76 A resolution crystal structure of glycogen phosphorylase B complexed with glucose, and CP320626, a potential antidiabetic drug.
- N. Oikonomakos, S. Zographos, V. Skamnaki, G. Archontis
- Chemistry, Medicine
- Bioorganic & medicinal chemistry
- 1 May 2002
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 muscle… Expand
Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase
Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and… Expand