High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor

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

(2021) Christoph Gorgulla et al.   iScience

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

(2021) Arvind Ramanathan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2

(2021) Nir Drayman et al.   SCIENCE

Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease

(2021) Maya G. Deshmukh et al.   STRUCTURE

Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency

(2021) Chun-Hui Zhang et al.   ACS Medicinal Chemistry Letters

Sub-Micromolar Inhibition of SARS-CoV-2 3CLpro by Natural Compounds

(2021) Bruno Rizzuti et al.   Pharmaceuticals

Design and Performance Characterization of RADICAL-Pilot on Leadership-Class Platforms

(2021) Andre Merzky et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

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

(2020) Zhenming Jin et al.   NATURE

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

(2020) Linlin Zhang et al.   SCIENCE

Drug discovery strategies for SARS-CoV-2

(2020) Zeenat A Shyr et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease

(2020) Emanuelle Machado Marinho et al.   MICROBIAL PATHOGENESIS

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice

(2020) Athri D. Rathnayake et al.   Science Translational Medicine

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

(2020) Daniel W. Kneller et al.   Nature Communications

A molecular docking study repurposes FDA approved iron oxide nanoparticles to treat and control COVID-19 infection

(2020) Yasmin Abo-zeid et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

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

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

Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19

(2020) Robert L. Hoffman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Evolution of the COVID-19 vaccine development landscape

(2020) Tung Thanh Le et al.   NATURE REVIEWS DRUG DISCOVERY

High-resolution structures of the SARS-CoV-2 2′-O-methyltransferase reveal strategies for structure-based inhibitor design

(2020) Monica Rosas-Lemus et al.   Science Signaling

Malleability of the SARS-CoV-2 3CL Mpro active site cavity facilitates binding of clinical antivirals

(2020) Daniel W. Kneller et al.   STRUCTURE

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication

(2020) Wayne Vuong et al.   Nature Communications

Room-temperature neutron and X-ray data collection of 3CL Mpro from SARS-CoV-2

(2020) Daniel W. Kneller et al.   Acta Crystallographica Section F-Structural Biology Communications

Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design

(2020) Daniel W. Kneller et al.   IUCrJ

Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain

(2020) Arvind Ramanathan et al.   Biomolecules

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

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

Oxford–AstraZeneca COVID-19 vaccine efficacy

(2020) Maria Deloria Knoll et al.   LANCET

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations

(2018) Akash Parvatikar et al.   BIOPHYSICAL JOURNAL

Author Correction: VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration

(2017) Nafisa M. Hassan et al.   Scientific Reports

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy

(2016) Thanigaimalai Pillaiyar et al.   JOURNAL OF MEDICINAL CHEMISTRY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

An open port sampling interface for liquid introduction atmospheric pressure ionization mass spectrometry

(2015) Gary J. Van Berkel et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

FRED and HYBRID docking performance on standardized datasets

(2012) Mark McGann   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Discovering Conformational Sub-States Relevant to Protein Function

(2011) Arvind Ramanathan et al.   PLoS One

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

(2010) Jonathan B. Baell et al.   JOURNAL OF MEDICINAL CHEMISTRY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

DOVIS: an implementation for high-throughput virtual screening using AutoDock

(2008) Shuxing Zhang et al.   BMC BIOINFORMATICS