Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches

RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics

(2022) Daniel Platero-Rochart et al.   BIOINFORMATICS

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

(2021) Diogo Santos-Martins et al.   Journal of Chemical Theory and Computation

A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening

(2021) Christoph Gorgulla et al.   iScience

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

(2021) Guoli Xiong et al.   NUCLEIC ACIDS RESEARCH

AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability

(2021) Pierre Darme et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization

(2021) Christoph Gorgulla et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening

(2021) Aayush Gupta et al.   Journal of Chemical Information and Modeling

PyRMD: A New Fully Automated AI-Powered Ligand-Based Virtual Screening Tool

(2021) Giorgio Amendola et al.   Journal of Chemical Information and Modeling

Machine learning models for classification tasks related to drug safety

(2021) Anita Rácz et al.   MOLECULAR DIVERSITY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Synthon-based ligand discovery in virtual libraries of over 11 billion compounds

(2021) Arman A. Sadybekov et al.   NATURE

A practical guide to large-scale docking

(2021) Brian J. Bender et al.   Nature Protocols

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

(2020) Reed M. Stein et al.   NATURE

ChEMBL-Likeness Score and Database GDBChEMBL

(2020) Sven Bühlmann et al.   Frontiers in Chemistry

An open-source drug discovery platform enables ultra-large virtual screens

(2020) Christoph Gorgulla et al.   NATURE

Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery

(2020) Francesco Gentile et al.   ACS Central Science

High-Throughput Docking Using Quantum Mechanical Scoring

(2020) Claudio N. Cavasotto et al.   Frontiers in Chemistry

Bayer’s in silico ADMET platform: a journey of machine learning over the past two decades

(2020) Andreas H. Göller et al.   DRUG DISCOVERY TODAY

Improved Scaffold Hopping in Ligand-based Virtual Screening Using Neural Representation Learning

(2020) Luka Stojanović et al.   Journal of Chemical Information and Modeling

Machine learning classification can reduce false positives in structure-based virtual screening

(2020) Yusuf O. Adeshina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can easy chemistry produce complex, diverse, and novel molecules?

(2020) Anna Tomberg et al.   DRUG DISCOVERY TODAY

Generating multibillion chemical space of readily accessible screening compounds

(2020) Oleksandr O. Grygorenko et al.   iScience

LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening

(2020) Maximilian Grimm et al.   Journal of Chemical Information and Modeling

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

(2020) A. Acharya et al.   Journal of Chemical Information and Modeling

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?

(2019) Wilfredo Evangelista Falcon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ADMET modeling approaches in drug discovery

(2019) Leonardo L.G. Ferreira et al.   DRUG DISCOVERY TODAY

Single-particle cryo-EM studies of transmembrane proteins in SMA copolymer nanodiscs

(2019) Chang Sun et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Targeted protein degradation: elements of PROTAC design

(2019) Stacey-Lynn Paiva et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

An Overview of Machine Learning and Big Data for Drug Toxicity Evaluation

(2019) Andy H. Vo et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Recent applications of machine learning in medicinal chemistry

(2018) Jane Panteleev et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A big data approach to the concordance of the toxicity of pharmaceuticals in animals and humans

(2018) Matthew Clark et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis

(2018) Yunyi Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

GPU Accelerated Quantum Virtual Screening: Application for the Natural Inhibitors of New Dehli Metalloprotein (NDM-1)

(2018) Mingsong Shi et al.   Frontiers in Chemistry

SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening

(2016) Vincent Zoete et al.   Journal of Chemical Information and Modeling

Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories

(2016) Song Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Empirical Scoring Functions for Affinity Prediction of Protein-ligand Complexes

(2016) Lukas P. Pason et al.   Molecular Informatics

Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools

(2015) L. Tao et al.   ADVANCED DRUG DELIVERY REVIEWS

LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors

(2015) Samo Lešnik et al.   Journal of Chemical Information and Modeling

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions

(2015) Zhuo Yang et al.   JOURNAL OF MOLECULAR MODELING

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

(2015) Sergio Decherchi et al.   Nature Communications

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

(2013) Guo-Bo Li et al.   Journal of Chemical Information and Modeling

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Ligand-Based Virtual Screening Approach Using a New Scoring Function

(2012) Adel Hamza et al.   Journal of Chemical Information and Modeling

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain

(2012) Antje Wolf et al.   JOURNAL OF MOLECULAR MODELING

ZINCPharmer: pharmacophore search of the ZINC database

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success

(2009) Frank Lovering et al.   JOURNAL OF MEDICINAL CHEMISTRY

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

(2009) Lorenz C. Blum et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How do bacterial cells ensure that metalloproteins get the correct metal?

(2008) Kevin J. Waldron et al.   NATURE REVIEWS MICROBIOLOGY