pmx: Automated protein structure and topology generation for alchemical perturbations

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Computational design of protein–protein interactions

(2013) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

(2012) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Recent advances in computational protein design

(2011) Robert J Pantazes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Towards computional specificity screening of DNA-binding proteins

(2011) Daniel Seeliger et al.   NUCLEIC ACIDS RESEARCH

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

(2010) Daniel Seeliger et al.   BIOPHYSICAL JOURNAL

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

A three-state prediction of single point mutations on protein stability changes

(2008) Emidio Capriotti et al.   BMC BIOINFORMATICS

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS