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Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

Journal of chemical information and modeling, 2017-09, Vol.57 (9), p.2203-2221

2017

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Accurate calculation of the absolute free energy of binding for drug molecules

Chemical science (Cambridge), 2016-01, Vol.7 (1), p.207-218

2016

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Therapeutic Potential of Targeting Plasminogen Activator Inhibitor-1 in COVID-19

Trends in pharmacological sciences (Regular ed.), 2021-06, Vol.42 (6), p.431-433

2021

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Design of the Global Health chemical diversity library v2 for screening against infectious diseases

PLoS neglected tropical diseases, 2023-12, Vol.17 (12), p.e0011799

2023

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Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

Journal of the American Chemical Society, 2017-01, Vol.139 (2), p.946-957

2017

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Small-molecule modulators of serine protease inhibitor proteins (serpins)

Drug discovery today, 2021-02, Vol.26 (2), p.442-454

2021

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Comparing global and local likelihood score thresholds in multiclass laplacian-modified Naive Bayes protein target prediction

Combinatorial chemistry & high throughput screening, 2015-01, Vol.18 (3), p.323-330

2015

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Development and Application of a Data-Driven Reaction Classification Model: Comparison of an Electronic Lab Notebook and Medicinal Chemistry Literature

Journal of chemical information and modeling, 2019-10, Vol.59 (10), p.4167-4187

2019

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Guiding lead optimization with GPCR structure modeling and molecular dynamics

Current opinion in pharmacology, 2016-10, Vol.30, p.14-21

2016

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RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design

Molecular informatics, 2022-04, Vol.41 (4), p.e2100207-n/a

2022

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Enhancing reaction-based de novo design using a multi-label reaction class recommender

Journal of computer-aided molecular design, 2020-07, Vol.34 (7), p.783-803

2020

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Knowledge-Based Approach to de Novo Design Using Reaction Vectors

Journal of Chemical Information and Modeling, 2009-05, Vol.49 (5), p.1163-1184

2009

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Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors

Molecular informatics, 2024-04, Vol.43 (4), p.e202300183-n/a

2024

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Characterizing Interhelical Interactions of G‑Protein Coupled Receptors with the Fragment Molecular Orbital Method

Journal of chemical theory and computation, 2020-04, Vol.16 (4), p.2814-2824

2020

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Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties

Advances in experimental medicine and biology, 2016, Vol.922, p.161-181

2016

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Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Communications chemistry, 2018-04, Vol.1 (1), Article 19

2018

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Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat

ACS chemical biology, 2017-06, Vol.12 (6), p.1593-1602

2017

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3D QSAR Methods: Phase and Catalyst Compared

Journal of chemical information and modeling, 2007-05, Vol.47 (3), p.1248-1257

2007

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Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis

Molecular bioSystems, 2015-01, Vol.11 (1), p.86-96

2015

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Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts

Future medicinal chemistry, 2014-01, Vol.6 (18), p.2029-2056

2014

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Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts

Molecular informatics, 2013-12, Vol.32 (11-12), p.1009-1024

2013

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Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis

MedChemComm, 2014-03, Vol.5 (3), p.386-396

2014

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Janocchio-a Java applet for viewing 3D structures and calculating NMR couplings and NOEs

Magnetic resonance in chemistry, 2007-07, Vol.45 (7), p.595-600

2007

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Predicting Ligand Selectivity Across Bromodomain Families

Biophysical journal, 2016-02, Vol.110 (3), p.545a-545a

2016

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Accurate calculation of the absolute free energy of binding for drug moleculesElectronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02678d

2015-12

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Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

Accurate calculation of the absolute free energy of binding for drug molecules

Therapeutic Potential of Targeting Plasminogen Activator Inhibitor-1 in COVID-19

Design of the Global Health chemical diversity library v2 for screening against infectious diseases

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

Small-molecule modulators of serine protease inhibitor proteins (serpins)

Comparing global and local likelihood score thresholds in multiclass laplacian-modified Naive Bayes protein target prediction

Development and Application of a Data-Driven Reaction Classification Model: Comparison of an Electronic Lab Notebook and Medicinal Chemistry Literature

Guiding lead optimization with GPCR structure modeling and molecular dynamics

RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design

Enhancing reaction-based de novo design using a multi-label reaction class recommender

Knowledge-Based Approach to de Novo Design Using Reaction Vectors

Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors

Characterizing Interhelical Interactions of G‑Protein Coupled Receptors with the Fragment Molecular Orbital Method

Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat

3D QSAR Methods: Phase and Catalyst Compared

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts

Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts

Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis

Janocchio-a Java applet for viewing 3D structures and calculating NMR couplings and NOEs

Predicting Ligand Selectivity Across Bromodomain Families

Accurate calculation of the absolute free energy of binding for drug moleculesElectronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02678d

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