@procacci61

Computational chemist, University of Florence (Italy), Dept. of Chemistry, the raft is mine

Joined December 2016
  • Tweets118
  • Following97
  • Followers111
42Media
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…
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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…
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Neat work by the Zhaoxi Sun team from Shen Zhen University on Cyclodextrin host-guest binding affinities prediction using noneq alchemy with vDSSB advanced.onlinelibrary.wiley…

Achieving Chemical Accuracy in Cyclodextrin Host–Guest Binding via Integrative Atomistic Modelling

A generalizable computational framework is presented that overcomes long-standing challenges in modelling cyclodextrin host-guest binding by integrating host-specific force-field refinement, equili...

advanced.onlinelibrary.wiley.com
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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/10.102…

Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment...

Abstract. We assess the performance of the nonequilibrium alchemical fast-growth method in calculating water and 1-octanol solvation free energies, compari

pubs.acs.org
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Ultrasensitive Detection of FKBP12 Using a Synthetic Receptor‐Functionalized QCM Nanoplatform - Tozzetti - Advanced Sensor Research - Wiley Online Library advanced.onlinelibrary.wiley…

Ultrasensitive Detection of FKBP12 Using a Synthetic Receptor‐Functionalized QCM Nanoplatform

A reusable nanosensor platform for ultralow FKBP12 detection in physiological fluids is presented. Combining a gold-coated QCM with a custom-designed receptor in a self-assembled monolayer, the...

advanced.onlinelibrary.wiley.com
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mdpi.com/2079-4991/15/16/123…

Combining QCM and SERS on a Nanophotonic Chip: A Dual-Functional Sensor for Biomolecular Interact...

We present a dual biosensing strategy integrating Quartz Crystal Microbalance (QCM) and Surface-Enhanced Raman Spectroscopy (SERS) for the quantitative and molecular-specific detection of FKBP12....

mdpi.com
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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/1745…

chat_me_DeepSeek_on_alchemy.pdf

drive.google.com
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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…
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A contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest #SAMPL @samplchallenges pubs.rsc.org/en/content/arti…
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Piero Procacci retweeted
ChemMedChem@ChemMedChem24 May 2024
#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/…
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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…
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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

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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.
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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/acs… #compchem @ENEAOfficial @samplchallenges

Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics...

Abstract. In this study, we have tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter standard MD simulations, and

pubs.acs.org
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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
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LogP(tw) SAMPL9 analysis at procacci.github.io/LogP-SAMP… #compchem @samplchallenges
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Our paper on relative dissociation free energies with #GROMACS between dissimilar molecules tested on #SAMPL9 is finally out onlinelibrary.wiley.com/doi/…. Check out the tutorial procacci.github.io/vdssb_gro… and toolkit and data at zenodo.org/record/6982932 #compchem @Cineca1969
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LogP (toluene-water) SAMPL9 prediction using Fast Growth nonequilibrium alchemy on #CRESCO6 tinyurl.com/mwxz5x5e #compchem @samplchallenges @ENEAOfficial
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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
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Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations? mdpi.com/1420-3049/27/14/442… on APA molecule with solvent-modulated E/Z competition #compchem @MDPIOpenAccess @samplchallenges @UTICT.ENEA.IT @Schrodinger
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