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Theoretical and Computational Chemistry

Working Paper

Assessing Methods and Obstacles in Chemical Space Exploration

Shawn Reeves, Benjamin DiFrancesco, Vijay Shahani, Stephen S. MacKinnon, Andreas Windemuth, Andrew E. Brereton

Version 3 posted 23 October 2020

692

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Theoretical and Computational Chemistry

Working Paper

Generate, Repurpose, Validate: A Receptor-Mediated Atom-by-Atom Drug Generation for SARS-Cov-2 Spike Protein and Similarity-Mapped Drug Repurposing for COVID-19 with Rigorous Free Energy Validation Using Well-Tempered Metadynamics

Rituparno Chowdhury, Venkata Sai Sreyas Adury, Amal Vijay, Reman K. Singh, Arnab Mukherjee

Version 1 posted 18 May 2020

1,077

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2

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Analytical Chemistry

Working Paper

GenUI: Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation

Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen

Version 2 posted 08 June 2021

1,103

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Theoretical and Computational Chemistry

Working Paper

Generate What You Can Make: Achieving in-house synthesizability with readily available resources in de novo drug design

Alan Kai Hassen, Martin Sicho, Yorick J. van Aalst, Mirjam C.W. Huizenga, Darcy N.R. Reynolds, Sohvi Luukkonen, Andrius Bernatavicius, Djork-Arné Clevert, Antonius P.A. Janssen, Gerard J.P. van Westen, Mike Preuss

Version 1 posted 05 March 2024

890

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1

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Theoretical and Computational Chemistry

Working Paper

AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

Andrius Bernatavicius, Martin Šícho, Antonius Janssen, Alan Kai Hassen, Mike Preuss, Gerard van Westen

Version 2 posted 18 April 2024

933

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Theoretical and Computational Chemistry

Working Paper

SmilesFormer: Language Model for Molecular Design

Joshua Owoyemi, Nazim Medzhidov

Version 1 posted 03 May 2023

283

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Theoretical and Computational Chemistry

Working Paper

fragSMILES: a Chemical String Notation for Advanced Fragment and Chirality Representation

Fabrizio Mastrolorito, Fulvio Ciriaco, Maria Vittoria Togo, Nicola Gambacorta, Daniela Trisciuzzi, Cosimo Damiano Altomare, Nicola Amoroso, Francesca Grisoni, Orazio Nicolotti

Version 2 posted 23 July 2024

317

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Theoretical and Computational Chemistry

Working Paper

Individual & Collective Human Intelligence in Drug Design: Evaluating the Search Strategy

Giovanni Cincilla, Simone Masoni, Jascha Blobel

Version 2 posted 18 March 2021

650

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Theoretical and Computational Chemistry

Working Paper

Tree-Invent: A novel molecular generative model constrained with topological tree

Mingyuan Xu, HongMing Chen

Version 1 posted 29 March 2023

443

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Biological and Medicinal Chemistry

Working Paper

UnCorrupt SMILES: a novel approach to de novo design

Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen

Version 2 posted 14 November 2022

501

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15 results in De novo drug design in Keywords: De novo drug design

Assessing Methods and Obstacles in Chemical Space Exploration

Generate, Repurpose, Validate: A Receptor-Mediated Atom-by-Atom Drug Generation for SARS-Cov-2 Spike Protein and Similarity-Mapped Drug Repurposing for COVID-19 with Rigorous Free Energy Validation Using Well-Tempered Metadynamics

GenUI: Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation

Generate What You Can Make: Achieving in-house synthesizability with readily available resources in de novo drug design

AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

SmilesFormer: Language Model for Molecular Design

fragSMILES: a Chemical String Notation for Advanced Fragment and Chirality Representation

Individual & Collective Human Intelligence in Drug Design: Evaluating the Search Strategy

Tree-Invent: A novel molecular generative model constrained with topological tree

UnCorrupt SMILES: a novel approach to de novo design

15 results in Keywords: De novo drug design