Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

(2021) Emma C. Thomson et al.   CELL

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

(2021) Kevin R. McCarthy et al.   SCIENCE

SARS-CoV-2 mRNA Vaccines: Immunological Mechanism and Beyond

(2021) Emily Bettini et al.   Vaccines

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

(2021) Nuno R. Faria et al.   SCIENCE

Convergent evolution of SARS-CoV-2 in human and animals

(2021) Hang-Yu Zhou et al.   Protein & Cell

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

(2021) Fernando González-Candelas et al.   INFECTION GENETICS AND EVOLUTION

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

(2020) Aiping Wu et al.   Cell Host & Microbe

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis

(2020) Derek K Chu et al.   LANCET

Performance and Its Limits in Rigid Body Protein-Protein Docking

(2020) Israel T. Desta et al.   STRUCTURE

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships

(2019) Ahmad Abu Turab Naqvi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structural, functional, and stability change predictions in human telomerase upon specific point mutations

(2019) U. Kalathiya et al.   Scientific Reports

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: a comparative docking and MD simulation studies

(2018) Mehak Gulzar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

PDBsum: Structural summaries of PDB entries

(2017) Roman A. Laskowski et al.   PROTEIN SCIENCE

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study

(2016) Jiraphorn Phanich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Amino Acid Substitutions That Affect Receptor Binding and Stability of the Hemagglutinin of Influenza A/H7N9 Virus

(2016) Eefje J. A. Schrauwen et al.   JOURNAL OF VIROLOGY

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site

(2014) Yuan Xie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Single Amino Acid in the Stalk Region of the H1N1pdm Influenza Virus HA Protein Affects Viral Fusion, Stability and Infectivity

(2014) Christopher R. Cotter et al.   PLoS Pathogens

Coronaviruses as DNA Wannabes: A New Model for the Regulation of RNA Virus Replication Fidelity

(2013) Everett Clinton Smith et al.   PLoS Pathogens

Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity

(2010) Jeong Chan Joo et al.   JOURNAL OF BIOTECHNOLOGY