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Optimizing interactions to protein binding sites by integrating docking-scoring strategies into generative AI methods

Frontiers in chemistry, 2022-10, Vol.10, p.1012507

2022

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Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints

Structure (London), 2015-12, Vol.23 (12), p.2280-2290

2015

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3D-Lab: a collaborative web-based platform for molecular modeling

Future medicinal chemistry, 2016-09, Vol.8 (14), p.1739-1752

2016

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Integrating Reaction Schemes, Reagent Databases, and Virtual Libraries into Fragment-Based Design by Reinforcement Learning

Journal of chemical information and modeling, 2023-09, Vol.63 (18), p.5709-5726

2023

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Virtual Screening in the Cloud: How Big Is Big Enough?

Journal of chemical information and modeling, 2020-09, Vol.60 (9), p.4274-4282

2020

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Automated De Novo Design in Medicinal Chemistry: Which Types of Chemistry Does a Generative Neural Network Learn?

Journal of medicinal chemistry, 2020-08, Vol.63 (16), p.8809-8823

2020

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Modern machine‐learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges

Wiley interdisciplinary reviews. Computational molecular science, 2024-05, Vol.14 (3), p.e1716-n/a

2024

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Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence

Journal of chemical information and modeling, 2022-02, Vol.62 (3), p.447-462

2022

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Molecular Rift: Virtual Reality for Drug Designers

Journal of chemical information and modeling, 2015-11, Vol.55 (11), p.2475-2484

2015

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Application of Deep Neural Network Models in Drug Discovery Programs

ChemMedChem, 2021-12, Vol.16 (24), p.3772-3786

2021

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Tabu search based global optimization algorithms for problems in computational chemistry

Journal of cheminformatics, 2012-05, Vol.4 (Suppl 1), p.P10-P10, Article P10

2012

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Structural insight into allosteric modulation of protease-activated receptor 2

Nature (London), 2017-05, Vol.545 (7652), p.112-115

2017

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Task‐Similarity is a Crucial Factor for Few‐Shot Meta‐Learning of Structure‐Activity Relationships

Chembiochem : a European journal of chemical biology, 2024-10, Vol.25 (19), p.e202400095-n/a

2024

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Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design

Journal of chemical information and modeling, 2016-04, Vol.56 (4), p.774-787

2016

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Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions

Biophysical journal, 2017-03, Vol.112 (6), p.1147-1156

2017

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Efficiency of tabu-search-based conformational search algorithms

Journal of computational chemistry, 2011-07, Vol.32 (10), p.2245-2253

2011

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Impact of Applicability Domains to Generative Artificial Intelligence

ACS omega, 2023-06, Vol.8 (25), p.23148-23167

2023

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PathOpt-A global transition state search approach: Outline of algorithm

Journal of computational chemistry, 2013-08, Vol.34 (21), p.1810-1818

2013

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

Journal of chemical theory and computation, 2019-11, Vol.15 (11), p.6243-6253

2019

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Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis

Bioorganic & medicinal chemistry, 2016-10, Vol.24 (20), p.4855-4866

2016

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CAST: A new program package for the accurate characterization of large and flexible molecular systems

Journal of computational chemistry, 2014-09, Vol.35 (24), p.1801-1807

2014

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A New Tabu-Search-Based Algorithm for Solvation of Proteins

Journal of chemical theory and computation, 2013-01, Vol.9 (1), p.814-821

2013

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Force field-based conformational searches: efficiency and performance for peptide receptor complexes

Molecular physics, 2013-09, Vol.111 (16-17), p.2489-2500

2013

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Computational Approaches for Target Inference

Target Discovery and Validation, 2020

Plowright, Alleyn T

2020

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Interoperable communication for autonomous mobile robots: Enabling multimodal information exchange

Atp-Edition : automatisierungstechnische Praxis, 2024-03, Vol.66 (3), p.76-84

2024

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Optimizing interactions to protein binding sites by integrating docking-scoring strategies into generative AI methods

Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints

3D-Lab: a collaborative web-based platform for molecular modeling

Integrating Reaction Schemes, Reagent Databases, and Virtual Libraries into Fragment-Based Design by Reinforcement Learning

Virtual Screening in the Cloud: How Big Is Big Enough?

Automated De Novo Design in Medicinal Chemistry: Which Types of Chemistry Does a Generative Neural Network Learn?

Modern machine‐learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges

Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence

Molecular Rift: Virtual Reality for Drug Designers

Application of Deep Neural Network Models in Drug Discovery Programs

Tabu search based global optimization algorithms for problems in computational chemistry

Structural insight into allosteric modulation of protease-activated receptor 2

Task‐Similarity is a Crucial Factor for Few‐Shot Meta‐Learning of Structure‐Activity Relationships

Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design

Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions

Efficiency of tabu-search-based conformational search algorithms

Impact of Applicability Domains to Generative Artificial Intelligence

PathOpt-A global transition state search approach: Outline of algorithm

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

Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis

CAST: A new program package for the accurate characterization of large and flexible molecular systems

A New Tabu-Search-Based Algorithm for Solvation of Proteins

Force field-based conformational searches: efficiency and performance for peptide receptor complexes

Computational Approaches for Target Inference

Interoperable communication for autonomous mobile robots: Enabling multimodal information exchange

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