Piero Procacci @procacci61
Computational chemist, University of Florence (Italy), Dept. of Chemistry, the raft is mine Joined December 2016-
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Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6–31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches | Journal of Chemical Theory and Computation pubs.acs.org/doi/full/10.10…
Ultrasensitive Detection of FKBP12 Using a Synthetic Receptor‐Functionalized QCM Nanoplatform - Tozzetti - Advanced Sensor Research - Wiley Online Library advanced.onlinelibrary.wiley.com/doi/full/10.10…
Very interesting chat between me and DeepSeek on alchemical methods for binding free energy calculations #compchem #drugdesign Anyone interested can find the chat here: drive.google.com/file/d/17458HN…
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/pdbrestor…
A contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest #SAMPL @samplchallenges pubs.rsc.org/en/content/art…
#OnTheCover Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations (ChemMedChem 10/2024) (P. Procacci et al.) @procacci61 onlinelibrary.wiley.com/doi/10.1002/cm…
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 …mistry-europe.onlinelibrary.wiley.com/doi/10.1002/cm…
At Lidea, we are developing collaborative, cross-functional working methods and a culture of innovation that is supported by representatives from each country and department. #Insiders
Addressing Suboptimal Poses using HREM combined with Nonequilibrium Alchemical Calculations with #GROMACS and #plumed. pubs.acs.org/doi/10.1021/ac… Full data (mdp-, top-, gro-files, and ancillary scripts) are available at zenodo.org/records/8377371.
Dealing (on #cresco6) with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions. Open Access at pubs.acs.org/doi/10.1021/ac… #compchem @ENEAOfficial @samplchallenges
Nonequilibrium fast-growth (NE-FG) blind prediction for LogP toluene/water partition coefficients published on the JCP aip.scitation.org/doi/10.1063/5.… #compchem @samplchallenges @ENEAOfficial
LogP(tw) SAMPL9 analysis at procacci.github.io/LogP-SAMPL9/ #compchem @samplchallenges
Our paper on relative dissociation free energies with #GROMACS between dissimilar molecules tested on #SAMPL9 is finally out onlinelibrary.wiley.com/doi/10.1002/jc…. Check out the tutorial procacci.github.io/vdssb_gromacs/… and toolkit and data at zenodo.org/record/6982932 #compchem @Cineca1969
LogP (toluene-water) SAMPL9 prediction using Fast Growth nonequilibrium alchemy on #CRESCO6 tinyurl.com/mwxz5x5e #compchem @samplchallenges @ENEAOfficial
RBFE with #GROMACS between dissimilar molecules using bidirectional #nonequilibrium dual topology schemes. Zenodo link zenodo.org/record/6850702 with all you need (except maybe the HPC) to test the method on the WP6 guests of the #SAMPL 9 challenge. #compchem @PRACE_RI @Cineca1969
Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations? mdpi.com/1420-3049/27/1… on APA molecule with solvent-modulated E/Z competition #compchem @MDPIOpenAccess @samplchallenges @UTICT.ENEA.IT @schrodinger
Nonequilibrium RBFE between chemically distant compounds (different volume, small Tanimoto, different net charge) published on the JCTC pubs.acs.org/doi/10.1021/ac…. Testbed on SAMPL9 #compchem @samplchallenges @ENEAOfficial
Our paper on the #SAMPL9 challenge within an analysis of ranked submissions is finally out on the JCP. aip.scitation.org/doi/10.1063/5.… #compchem @samplchallenges @ENEAOfficial
#chemrxiv NonEq-RBFE for #SAMPL9 chemrxiv.org/engage/chemrxi…. NE-RBFE bypasses limitations of the #FEP-based #RBFE, such as slowly relaxing water, sampling issues on intermediate l, no scaffold hopping. #compchem @drugdesigndata @samplchallenges.
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