A Structurally Flexible Protein Backbone for the MARTINI Coarse Grained Force Field

Protein-Ligand Binding Simulation with t

Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Field

✍ Negami, Tatsuki; Shimizu, Kentaro; Terada, Tohru 📂 Article 📅 2014 🏛 Biophysical Society 🌐 English ⚖ 40 KB

Covering All the Bases: A Martini Coarse

Covering All the Bases: A Martini Coarse-Grained Force Field for DNA

✍ Uusitalo, Jaakko J.; Ingólfsson, Helgi I.; Marrink, Siewert-Jan 📂 Article 📅 2013 🏛 Biophysical Society 🌐 English ⚖ 102 KB

Coarse-graining polymers with the MARTIN

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

✍ Rossi, Giulia ;Monticelli, Luca ;Puisto, Sakari R. ;Vattulainen, Ilpo ;Ala-Nissi 📂 Article 📅 2011 🏛 Royal Society of Chemistry 🌐 English ⚖ 175 KB

Statistical theory for protein combinato

Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure

✍ Hidetoshi Kono; Jeffery G. Saven 📂 Article 📅 2001 🏛 Elsevier Science 🌐 English ⚖ 689 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

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