An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain

Conversion from a virtual-bond chain to

Conversion from a virtual-bond chain to a complete polypeptide backbone chain

✍ Enrico O. Purisima; Harold A. Scheraga 📂 Article 📅 1984 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 955 KB

## Abstract A method for generating a complete polypeptide backbone structure from a set of C^α^ coordinates is presented. Initial trial values of ϕ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual‐bond backbone, e.g., and α‐hel

Rapid and Quantitative Disulfide Bond Fo

Rapid and Quantitative Disulfide Bond Formation for a Polypeptide Chain Using a Cyclic Selenoxide Reagent in an Aqueous Medium

✍ Kenta Arai; Dr. Kenichi Dedachi; Prof. Dr. Michio Iwaoka 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 249 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. I. The method

✍ Urszula Kozłowska; Adam Liwo; Harold A. Scheraga 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 381 KB 👁 1 views

## Abstract In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simula

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