Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

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

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

(2021) Chun-Hui Zhang et al.   ACS Central Science

Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography

(2021) Daniel W. Kneller et al.   JOURNAL OF MEDICINAL CHEMISTRY

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Ligand‐centered assessment of SARS‐CoV‐2 drug target models in the Protein Data Bank

(2020) Alexander Wlodawer et al.   FEBS Journal

Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds

(2020) André Fischer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition

(2020) Aleix Gimeno et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease

(2020) Chinmayee Choudhury   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring

(2020) Wen-Ling Ye et al.   Journal of Chemical Information and Modeling

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations

(2020) Hugo Guterres et al.   Journal of Chemical Information and Modeling

Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial

(2020) Yeming Wang et al.   LANCET

Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study

(2020) Davide Gentile et al.   Marine Drugs

Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds

(2020) Anh-Tien Ton et al.   Molecular Informatics

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin et al.   NATURE

Citrus reticulata peel oil as an antiatherogenic agent: Hypolipogenic effect in hepatic cells, lipid storage decrease in foam cells, and prevention of LDL oxidation

(2020) María A. Castro et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy

(2020) Bhupesh Goyal et al.   ACS Combinatorial Science

COVID-19: Living through Another Pandemic

(2020) Essam Eldin A. Osman et al.   ACS Infectious Diseases

Identification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2

(2020) Pradeep Sharma et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease

(2020) Tanuja Joshi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses

(2020) Irina V. Gushchina et al.   Journal of Chemical Information and Modeling

In silico Drug Repurposing for COVID‐19: Targeting SARS‐CoV‐2 Proteins through Docking and Consensus Ranking

(2020) Claudio Cavasotto et al.   Molecular Informatics

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

Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy

(2020) Taj Mohammad et al.   VIRUS RESEARCH

Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates

(2020) Ryunosuke Yoshino et al.   Scientific Reports

Structure-based drug designing and immunoinformatics approach for SARS-CoV-2

(2020) Pritam Kumar Panda et al.   Science Advances

Structure-based virtual screening of phytochemicals and repurposing of FDA approved antiviral drugs unravels lead molecules as potential inhibitors of coronavirus 3C-like protease enzyme

(2020) Arun Bahadur Gurung et al.   JOURNAL OF KING SAUD UNIVERSITY SCIENCE

Active constituents and mechanisms of Respiratory Detox Shot, a traditional Chinese medicine prescription, for COVID-19 control and prevention: Network-molecular docking-LC–MSE analysis

(2020) Zi-jia Zhang et al.   Journal of Integrative Medicine-JIM

The SARS-CoV-2 main protease as drug target

(2020) Sven Ullrich et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography

(2020) Daniel W. Kneller et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling

(2020) Karina Kapusta et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening

(2020) Adib Ghaleb et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2

(2020) Mohammad M. Ghahremanpour et al.   ACS Medicinal Chemistry Letters

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

(2020) Alice Douangamath et al.   Nature Communications

Can drug repurposing strategies be the solution to the COVID-19 crisis?

(2020) Carolina L. Bellera et al.   Expert Opinion on Drug Discovery

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

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

Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease

(2020) Akshita Gupta et al.   ACS Omega

Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning

(2019) Nobuaki Yasuo et al.   Journal of Chemical Information and Modeling

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions

(2019) Jianing Lu et al.   Journal of Chemical Information and Modeling

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

(2019) Jeffrey A. van Santen et al.   ACS Central Science

Docking structurally similar analogues: Dealing with the false-positive

(2019) Zahara Khanjiwala et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark

(2018) Yan Li et al.   Nature Protocols

IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics

(2018) Karthikeyan Mohanraj et al.   Scientific Reports

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

(2018) Veronica Salmaso et al.   Frontiers in Pharmacology

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening

(2017) Spencer S. Ericksen et al.   Journal of Chemical Information and Modeling

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules

(2017) Esko Oksanen et al.   MOLECULES

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

SuperDRUG2: a one stop resource for approved/marketed drugs

(2017) Vishal B Siramshetty et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry

(2017) Ben Bax et al.   Acta Crystallographica Section D-Structural Biology

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fast, accurate, and reliable molecular docking with QuickVina 2

(2015) Amr Alhossary et al.   BIOINFORMATICS

ZINC 15 – Ligand Discovery for Everyone

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

Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function

(2014) Emily A. Golden et al.   AUSTRALIAN JOURNAL OF CHEMISTRY

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

(2013) S.F. Sousa et al.   CURRENT MEDICINAL CHEMISTRY

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

From methylene blue to chloroquine: a brief review of the development of an antimalarial therapy

(2012) Kristine Krafts et al.   PARASITOLOGY RESEARCH

Consensus virtual screening approaches to predict protein ligands

(2011) Andreas Kukol   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

(2011) Stefano Forli et al.   JOURNAL OF MEDICINAL CHEMISTRY

TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico

(2011) Calvin Yu-Chian Chen   PLoS One

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

(2010) Anna S. Gardberg et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase

(2009) Kirk E. Hevener et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Virtual Screening Using PLS Discriminant Analysis and ROC Curve Approach: An Application Study on PDE4 Inhibitors

(2008) Andrea Rizzi et al.   Journal of Chemical Information and Modeling