Software development papers¶

PPI-PELE: Monte Carlo simulations using PELE to identify a protein-protein inhibitor binding site and pose¶

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Paper: https://pubs.rsc.org/en/content/articlelanding/2020/ra/d0ra01127d

Frag-PELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design¶

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Paper: https://www.ncbi.nlm.nih.gov/pubmed/32027130

MSM-PELE: A Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies.¶

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Paper: https://www.ncbi.nlm.nih.gov/pubmed/31589430

Adaptive-PELE towards interactive protein-ligand modeling¶

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Paper: https://www.nature.com/articles/s41598-017-08445-5

AquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of buried Water Molecules in Proteins.¶

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Paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00925

DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs¶

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Paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00306

Exploring the Conformational Landscape of Bioactive Small Molecules¶

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Paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00304

Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug Discovery¶

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Paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00305