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Chemical Structural Novelty: On-Targets and Off-Targets

Journal of medicinal chemistry, 2011-10, Vol.54 (19), p.6771-6785

2011

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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

Journal of computer-aided molecular design, 2019-06, Vol.33 (6), p.531-558

2019

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Structure- and Ligand-Based Virtual Screening on DUD‑E+: Performance Dependence on Approximations to the Binding Pocket

Journal of chemical information and modeling, 2020-09, Vol.60 (9), p.4296-4310

2020

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Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands

Journal of computer-aided molecular design, 2024-12, Vol.38 (1), p.33, Article 33

2024

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Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery

Journal of computer-aided molecular design, 2008-03, Vol.22 (3-4), p.147-159

2008

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ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

Journal of computer-aided molecular design, 2017-05, Vol.31 (5), p.419-439

2017

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Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction

Journal of chemical information and modeling, 2021-12, Vol.61 (12), p.5948-5966

2021

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Electrostatic-field and surface-shape similarity for virtual screening and pose prediction

Journal of computer-aided molecular design, 2019-10, Vol.33 (10), p.865-886

2019

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A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles

Journal of medicinal chemistry, 2023-02, Vol.66 (3), p.1955-1971

2023

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Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design

Journal of computer-aided molecular design, 2023-11, Vol.37 (11), p.519-535

2023

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Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design

Journal of computer-aided molecular design, 2024-12, Vol.38 (1), p.12-12, Article 12

2024

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Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock

Journal of computer-aided molecular design, 2015-06, Vol.29 (6), p.485-509

2015

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Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis

Journal of natural products (Washington, D.C.), 2022-06, Vol.85 (6), p.1449-1458

2022

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From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product

Journal of computer-aided molecular design, 2024-12, Vol.38 (1), p.19-19, Article 19

2024

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Unmasking the True Identity of Rapamycin’s Minor Conformer

Journal of natural products (Washington, D.C.), 2023-07, Vol.86 (7), p.1862-1869

2023

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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

Journal of computer-aided molecular design, 2019-06, Vol.33 (6), p.531-558

2019

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XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X‑ray Electron Density Maps

Journal of medicinal chemistry, 2020-09, Vol.63 (18), p.10509-10528

2020

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Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose

Journal of computer-aided molecular design, 2018-07, Vol.32 (7), p.731-757

2018

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Conformational Strain of Macrocyclic Peptides in Ligand–Receptor Complexes Based on Advanced Refinement of Bound-State Conformers

Journal of medicinal chemistry, 2021-03, Vol.64 (6), p.3282-3298

2021

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Protein function annotation by local binding site surface similarity

Proteins, structure, function, and bioinformatics, 2014-04, Vol.82 (4), p.679-694

2014

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Surface-based protein binding pocket similarity

Proteins, structure, function, and bioinformatics, 2011-09, Vol.79 (9), p.2746-2763

2011

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Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes

Journal of computer-aided molecular design, 2015-02, Vol.29 (2), p.101-112

2015

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Robust Ligand-Based Modeling of the Biological Targets of Known Drugs

Journal of medicinal chemistry, 2006-05, Vol.49 (10), p.2921-2938

2006

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Extrapolative prediction using physically-based QSAR

Journal of computer-aided molecular design, 2016-02, Vol.30 (2), p.127-152

2016

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Does your model weigh the same as a Duck?

Journal of computer-aided molecular design, 2012-01, Vol.26 (1), p.57-67

2012

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Chemical Structural Novelty: On-Targets and Off-Targets

Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

Structure- and Ligand-Based Virtual Screening on DUD‑E+: Performance Dependence on Approximations to the Binding Pocket

Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands

Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction

Electrostatic-field and surface-shape similarity for virtual screening and pose prediction

A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles

Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design

Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design

Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock

Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis

From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product

Unmasking the True Identity of Rapamycin’s Minor Conformer

Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X‑ray Electron Density Maps

Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose

Conformational Strain of Macrocyclic Peptides in Ligand–Receptor Complexes Based on Advanced Refinement of Bound-State Conformers

Protein function annotation by local binding site surface similarity

Surface-based protein binding pocket similarity

Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes

Robust Ligand-Based Modeling of the Biological Targets of Known Drugs

Extrapolative prediction using physically-based QSAR

Does your model weigh the same as a Duck?

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