Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors

A novel coronavirus outbreak of global health concern

(2020) Chen Wang et al.   LANCET

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

(2020) Shuai Xia et al.   CELL RESEARCH

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

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

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

Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients

(2020) Hai-xia Su et al.   ACTA PHARMACOLOGICA SINICA

Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations

(2020) Alessandro Grottesi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs

(2020) Zhe Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aflatoxin B1–Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures

(2019) Martin Klvana et al.   MOLECULES

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation

(2019) Eko Aditya Rifai et al.   Journal of Chemical Information and Modeling

ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins

(2017) Janez Konc et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Targeted Covalent Inhibitors for Drug Design

(2016) Thomas A. Baillie   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies

(2015) Renato A. Bauer   DRUG DISCOVERY TODAY

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites

(2015) Janez Konc et al.   Journal of Chemical Information and Modeling

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

New ways to boost molecular dynamics simulations

(2015) Elmar Krieger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

(2014) Evanthia Lionta et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

ClusCo: clustering and comparison of protein models

(2013) Michal Jamroz et al.   BMC BIOINFORMATICS

Optimization of Compound Ranking for Structure-Based Virtual Ligand Screening Using an Established FRED-Surflex Consensus Approach

(2013) Jiangfeng Du et al.   Chemical Biology & Drug Design

Hit Identification and Optimization in Virtual Screening: Practical Recommendations Based on a Critical Literature Analysis

(2013) Tian Zhu et al.   JOURNAL OF MEDICINAL CHEMISTRY

FRED and HYBRID docking performance on standardized datasets

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

KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

(2011) Simon Saubern et al.   Molecular Informatics

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

(2010) Jeremy R. Greenwood et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Profiling of Substrate Specificity of SARS-CoV 3CLpro

(2010) Chi-Pang Chuck et al.   PLoS One

Design, synthesis and antiviral efficacy of a series of potent chloropyridyl ester-derived SARS-CoV 3CLpro inhibitors

(2008) Arun K. Ghosh et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

(2008) J. Shi et al.   JOURNAL OF VIROLOGY