Atomistic De‐novo Inhibitor Generation‐Guided Drug Repurposing for SARS‐CoV‐2 Spike Protein with Free‐Energy Validation by Well‐Tempered Metadynamics

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

(2020) Michael Letko et al.   Nature Microbiology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2

(2020) Yadi Zhou et al.   Cell Discovery

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

(2020) Pritam Kumar Panda et al.   Science Advances

Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

(2019) Riccardo Capelli et al.   Journal of Chemical Theory and Computation

Molecular Origin of DNA Kinking by Transcription Factors

(2015) Reman Kumar Singh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

(2015) Dávid Bajusz et al.   Journal of Cheminformatics

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor

(2013) Xing-Yi Ge et al.   NATURE

Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy

(2013) Wilbee D. Sasikala et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Recognizing Pitfalls in Virtual Screening: A Critical Review

(2012) Thomas Scior 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

The spike protein of SARS-CoV — a target for vaccine and therapeutic development

(2009) Lanying Du et al.   NATURE REVIEWS MICROBIOLOGY

BLASTing small molecules--statistics and extreme statistics of chemical similarity scores

(2008) P. Baldi et al.   BIOINFORMATICS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS