Computational chemist, University of Florence (Italy), Dept. of Chemistry, the raft is mine
Joined December 2016
- Tweets119
- Following97
- Followers112
- Likes13K
One blob to rule them all: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference
#compchem #DrugDesign
doi.org/10.1021/acs.jctc.6c0…
My paper on ABFE calculations with dual topology #nonequilibrium alchemy using an LJ-blob as reference is on chemrxiv
chemrxiv.org/doi/full/10.264…
PDBrestore is online. It repairs protein PDB chains extracted from a local PDB file or a PDB file downloaded from rcsb.org. The web app adds H's, fills gaps, adds missing side chains, produces a solvated MD Box. Feedback and RT appreciated. www1.chim.unifi.it/orac/pdbr…
A contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest #SAMPL @samplchallenges pubs.rsc.org/en/content/arti…
Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations #CACHE @Cineca1969 #compchem
chemistry-europe.onlinelibra…
Addressing Suboptimal Poses using HREM combined with Nonequilibrium Alchemical Calculations with #GROMACS and #plumed.
pubs.acs.org/doi/10.1021/acs…
Full data (mdp-, top-, gro-files, and ancillary scripts) are available at zenodo.org/records/8377371.
Nonequilibrium fast-growth (NE-FG) blind prediction for LogP toluene/water partition coefficients published on the JCP aip.scitation.org/doi/10.106… #compchem @samplchallenges @ENEAOfficial