Software development papers
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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

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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

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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

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Adaptive-PELE towards interactive protein-ligand modeling
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- Paper: https://www.nature.com/articles/s41598-017-08445-5

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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

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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

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Exploring the Conformational Landscape of Bioactive Small Molecules
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- Paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00304

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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