Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

(2021) Carlos A. Ramos-Guzmán et al.   ACS Catalysis

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

(2020) Jasper Fuk-Woo Chan et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

A novel coronavirus outbreak of global health concern

(2020) Chen Wang et al.   LANCET

First Case of 2019 Novel Coronavirus in the United States

(2020) Michelle L. Holshue et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs

(2020) Sangeun Jeon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2020) Zhenming Jin et al.   NATURE

Remdesivir for the Treatment of Covid-19 — Preliminary Report

(2020) John H. Beigel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1

(2020) Neeltje van Doremalen et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease

(2020) Wenhao Dai et al.   SCIENCE

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

Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease

(2020) Chunlong Ma et al.   CELL RESEARCH

Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease

(2020) Son Tung Ngo et al.   Journal of Chemical Information and Modeling

Repositioning of 8565 Existing Drugs for COVID-19

(2020) Kaifu Gao et al.   Journal of Physical Chemistry Letters

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

(2020) Rohit Batra et al.   Journal of Physical Chemistry Letters

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

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

(2020) Sergio Decherchi et al.   CHEMICAL REVIEWS

Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease

(2020) Marina Macchiagodena et al.   Journal of Chemical Theory and Computation

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

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

(2020) Wayne Vuong et al.   Nature Communications

Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2

(2020) Dibyendu Mondal et al.   BIOCHEMISTRY

Coronavirus envelope protein: current knowledge

(2019) Dewald Schoeman et al.   Virology Journal

Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity

(2019) Nguyen Thanh Nguyen et al.   Journal of Chemical Information and Modeling

Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy

(2019) Son Tung Ngo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

(2018) Haiyang Zhang et al.   Journal of Chemical Information and Modeling

Force Field Benchmark of Amino Acids. 2. Partition Coefficients between Water and Organic Solvents

(2018) Haiyang Zhang et al.   Journal of Chemical Information and Modeling

How Ligand Protonation State Controls Water in Protein–Ligand Binding

(2018) Jack A. Henderson et al.   Journal of Physical Chemistry Letters

Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution

(2017) Son Tung Ngo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

(2016) Ulf Ryde et al.   CHEMICAL REVIEWS

Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work

(2016) Son Tung Ngo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computation of pH-dependent binding free energies

(2015) M. Olivia Kim et al.   BIOPOLYMERS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

(2013) Abil E. Aliev et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Curcumin Binds to Aβ1–40 Peptides and Fibrils Stronger Than Ibuprofen and Naproxen

(2012) Son Tung Ngo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

(2012) Samuel Genheden et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity

(2011) Man Hoang Viet et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Binding free energy calculations and biological testing of novel thiobarbiturates as inhibitors of the human NAD+dependent histone deacetylase Sirt2

(2011) Urszula Uciechowska et al.   MedChemComm

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations

(2009) F. Marty Ytreberg   JOURNAL OF CHEMICAL PHYSICS

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