Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble

Dependence of Protein Stability on the S

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme

✍ Sugita, Yuji; Kitao, Akio 📂 Article 📅 1998 🏛 Biophysical Society 🌐 English ⚖ 238 KB

Determination of side-chain-rotamer and

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field

✍ Urszula Kozłowska; Gia G. Maisuradze; Adam Liwo; Harold A. Scheraga 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 674 KB

## Abstract Using the harmonic‐approximation approach of the accompanying article and AM1 energy surfaces of terminally blocked amino‐acid residues, we determined physics‐based side‐chain rotamer potentials and the side‐chain virtual‐bond‐deformation potentials of 19 natural amino‐acid residues wit