Medicinal Chemistry ⚗️

Inspirational Works

A formally exact method for high-throughput absolute binding-free-energy calculations

Bian, Shao, Chipot, Cai, Fu

Nat Comput Sci, 5, 621–626 (2025)

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Augmenting large language models with chemistry tools

Bran, Cox, Schilter, Baldassari, White, Schwaller

Nat Mach Intell, 6, 525-535 (2024)

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CHARMM: the biomolecular simulation program

Brooks, Mackerell, Nilsson, Petrella, Roux, Won, Archontis, Bartels, Boresch, Caflisch, Caves, Cui, Dinner, Feig, Fischer, Gao, Hodoscek, Im, Kuczera, Lazaridis, Ma, Ovchinnikov, Paci, Pastor, Post, Pu, Schaefer, Tidor, Venable, Woodcock, Wu, Yang, York, Karplus

J Comput Chem, 30, 1545-614 (2009)

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SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

Bugnon, Röhrig, Goullieux, Perez, Daina, Michielin, Zoete

Nucleic Acids Res, 52, W324-W332 (2024)

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Navigating protein landscapes with a machine-learned transferable coarse-grained model

Charron, Bonneau, Pasos-Trejo, et al.

Nat. Chem., 17, 1284–1292 (2025)

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SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

Daina, Michielin, Zoete

Sci Rep, 7, 42717 (2017)

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Eastman, Swails, Chodera, McGibbon, Zhao, Beauchamp, Wang, Simmonett, Harrigan, Stern, Wiewiora, Brooks, Pande

PLoS Comput Biol, 13, e1005659 (2017)

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Computational protein–ligand docking and virtual drug screening with the AutoDock suite

Forli, Huey, Pique, et al.

Nat Protoc, 11, 905–919 (2016)

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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Genheden, Ryde

Expert Opin Drug Discov, 10, 449-61 (2015)

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Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Hanwell, Curtis, Lonie, Vandermeersch, Zurek, Hutchison

J Cheminform, 4, 17 (2012)

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Molecular Dynamics Simulation for All

Hollingsworth, Dror

Neuron, 99, 1129-1143 (2018)

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Huang, Rauscher, Nawrocki, et al.

Nat Methods, 14, 71–73 (2017)

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g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations

Kumari, Kumar, Open Source Drug Discovery Consortium, Lynn

J Chem Inf Model, 54, 1951-62 (2014)

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Lee, Cheng, Swails, Yeom, Eastman, Lemkul, Wei, Buckner, Jeong, Qi, Jo, Pande, Case, Brooks, MacKerell, Klauda, Im

J Chem Theory Comput, 12, 405-13 (2016)

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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Liu, Hwang, Burley, Nitsche, Southan, Walters, Gilson

Nucleic Acids Res, 53, D1633-D1644 (2025)

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Computational modeling of realistic cell membranes

Marrink, Corradi, Souza, Ingolfsson, Tieleman, Sansom

Chemical reviews, 119, 6184-6226 (2019)

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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

McGibbon, Beauchamp, Harrigan, Klein, Swails, Hernández, Schwantes, Wang, Lane, Pande

Biophys J, 109, 1528-32 (2015)

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High-throughput prediction of protein conformational distributions with subsampled AlphaFold2

Monteiro da Silva, Cui, Dalgarno, Lisi, Rubenstein

Nat Commun, 15, 2464 (2024)

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The Art and Science of Molecular Docking

Paggi, Pandit, Dror

Annu Rev Biochem, 93, 389-410 (2024)

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Scalable molecular dynamics on CPU and GPU architectures with NAMD

Phillips, Hardy, Maia, Stone, Ribeiro, Bernardi, Buch, Fiorin, Hénin, Jiang, McGreevy, Melo, Radak, Skeel, Singharoy, Wang, Roux, Aksimentiev, Luthey-Schulten, Kalé, Schulten, Chipot, Tajkhorshid

J Chem Phys, 153, 44130 (2020)

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pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures

Pires, Blundell, Ascher

J Med Chem, 58, 4066-72 (2015)

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Pronk, Páll, Schulz, Larsson, Bjelkmar, Apostolov, Shirts, Smith, Kasson, van der Spoel, Hess, Lindahl

Bioinformatics, 29, 845-54 (2013)

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Computational approaches streamlining drug discovery

Sadybekov, Katritch

Nature, 616, 673–685 (2023)

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MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

Siebenmorgen, Menezes, Benassou, et al.

Nat Comput Sci, 4, 367–378 (2024)

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Martini 3: a general purpose force field for coarse-grained molecular dynamics

Souza, Alessandri, Barnoud, et al.

Nat Methods, 18, 382–388 (2021)

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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Trott, Olson

J Comput Chem, 31, 455-61 (2010)

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CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

Vanommeslaeghe, Hatcher, Acharya, Kundu, Zhong, Shim, Darian, Guvench, Lopes, Vorobyov, Mackerell

J Comput Chem, 31, 671-90 (2010)

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Ab initio characterization of protein molecular dynamics with AI2BMD

Wang, He, Li, Bi, Cheng, Shen, Meng, Zhang, Liu, Shao

Nature, 635, 1019-1027 (2024)

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CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Wu, Cheng, Jo, Rui, Song, Dávila-Contreras, Qi, Lee, Monje-Galvan, Venable, Klauda, Im

J Comput Chem, 35, 1997-2004 (2014)

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Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions

Wu, Stein, Kao, Brown, Mchaourab

Nat Commun, 16, 7107 (2025)

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Density functionals with broad applicability in chemistry

Zhao, Truhlar

Acc Chem Res, 41, 157-67 (2008)

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Medicinal Chemistry ⚗️

Inspirational Works

A formally exact method for high-throughput absolute binding-free-energy calculations

Augmenting large language models with chemistry tools

CHARMM: the biomolecular simulation program

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

Navigating protein landscapes with a machine-learned transferable coarse-grained model

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Molecular Dynamics Simulation for All

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Computational modeling of realistic cell membranes

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

High-throughput prediction of protein conformational distributions with subsampled AlphaFold2

The Art and Science of Molecular Docking

Scalable molecular dynamics on CPU and GPU architectures with NAMD

pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Computational approaches streamlining drug discovery

MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

Martini 3: a general purpose force field for coarse-grained molecular dynamics

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

Ab initio characterization of protein molecular dynamics with AI2BMD

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions

Density functionals with broad applicability in chemistry

Lab Publications

Discussion