Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid–protein interface with a case study

(2021) Long-Can Mei et al.   BRIEFINGS IN BIOINFORMATICS

A machine learning method based on the genetic and world competitive contests algorithms for selecting genes or features in biological applications

(2021) Yosef Masoudi-Sobhanzadeh et al.   Scientific Reports

Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

(2020) Abdo A. Elfiky   LIFE SCIENCES

Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods

(2020) Canrong Wu et al.   Acta Pharmaceutica Sinica B

Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: Possible therapeutic implication in COVID-19

(2020) Anas Shamsi et al.   BIOSCIENCE REPORTS

Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach

(2020) Lovika Mittal et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms

(2020) Xinqiang Ding et al.   Journal of Chemical Theory and Computation

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

(2020) Yadi Zhou et al.   Cell Discovery

Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19

(2020) Yuan Huang et al.   ACTA PHARMACOLOGICA SINICA

Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm

(2020) Yosef Masoudi-Sobhanzadeh et al.   BMC BIOINFORMATICS

Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research

(2020) Zhiwei Feng et al.   BRIEFINGS IN BIOINFORMATICS

MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm

(2020) Qifeng Bai et al.   BRIEFINGS IN BIOINFORMATICS

Ethnomedicines of Indian origin for combating COVID-19 infection by hampering the viral replication: using structure-based drug discovery approach

(2020) Selvaraj Alagu Lakshmi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

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

Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease

(2020) Mahmoud Kandeel et al.   LIFE SCIENCES

Computational-based drug repurposing methods in COVID-19

(2020) Yosef Masoudi-Sobhanzadeh   BioImpacts

Applications of machine learning and artificial intelligence for Covid-19 (SARS-CoV-2) pandemic: A review

(2020) Samuel Lalmuanawma et al.   CHAOS SOLITONS & FRACTALS

Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches

(2020) Deep Bhowmik et al.   INFECTION GENETICS AND EVOLUTION

Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase

(2020) Mark Andrew White et al.   Journal of Physical Chemistry Letters

Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19

(2020) Lorane Izabel da Silva Hage-Melim et al.   LIFE SCIENCES

CoV3D: a database of high resolution coronavirus protein structures

(2020) Ragul Gowthaman et al.   NUCLEIC ACIDS RESEARCH

DockCoV2: a drug database against SARS-CoV-2

(2020) Ting-Fu Chen et al.   NUCLEIC ACIDS RESEARCH

GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences

(2020) Shuyi Fang et al.   NUCLEIC ACIDS RESEARCH

HIT-COVID, a global database tracking public health interventions to COVID-19

(2020) Qulu Zheng et al.   Scientific Data

A review on viral data sources and search systems for perspective mitigation of COVID-19

(2020) Anna Bernasconi et al.   BRIEFINGS IN BIOINFORMATICS

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach

(2020) Chandra Bhushan Mishra et al.   BRIEFINGS IN BIOINFORMATICS

SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets

(2020) Ali F Alsulami et al.   BRIEFINGS IN BIOINFORMATICS

DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses

(2020) Akanksha Rajput et al.   BRIEFINGS IN BIOINFORMATICS

A domain-based vaccine construct against SARS-CoV-2, the causative agent of COVID-19 pandemic: development of self-amplifying mRNA and peptide vaccines

(2020) Mohammad Mostafa Pourseif et al.   BioImpacts

HVIDB: a comprehensive database for human–virus protein–protein interactions

(2020) Xiaodi Yang et al.   BRIEFINGS IN BIOINFORMATICS

DBCOVP: A database of coronavirus virulent glycoproteins

(2020) Susrita Sahoo et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Bio-inspired optimization for the molecular docking problem: State of the art, recent results and perspectives

(2019) María Jesús García-Godoy et al.   APPLIED SOFT COMPUTING

Publisher Correction: Network-based prediction of drug combinations

(2019) Feixiong Cheng et al.   Nature Communications

FeatureSelect: a software for feature selection based on machine learning approaches

(2019) Yosef Masoudi-Sobhanzadeh et al.   BMC BIOINFORMATICS

DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy

(2019) Yosef Masoudi-Sobhanzadeh et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Drug databases and their contributions to drug repurposing

(2019) Yosef Masoudi-Sobhanzadeh et al.   GENOMICS

Trader as a new optimization algorithm predicts drug-target interactions efficiently

(2019) Yosef Masoudi-Sobhanzadeh et al.   Scientific Reports

CASTp 3.0: computed atlas of surface topography of proteins

(2018) Wei Tian et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Network-based approach to prediction and population-based validation of in silico drug repurposing

(2018) Feixiong Cheng et al.   Nature Communications

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide

(2017) Hiba Alogheli et al.   Journal of Chemical Information and Modeling

Virtual screening applications in short-chain dehydrogenase/reductase research

(2017) Katharina R. Beck et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Drug Repurposing Hub: a next-generation drug library and information resource

(2017) Steven M Corsello et al.   NATURE MEDICINE

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

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

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

CaFE: a tool for binding affinity prediction using end-point free energy methods

(2016) Hui Liu et al.   BIOINFORMATICS

3Drefine: an interactive web server for efficient protein structure refinement

(2016) Debswapna Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

Adaptive molecular docking method based on information entropy genetic algorithm

(2015) Zhengfu Li et al.   APPLIED SOFT COMPUTING

Middle East Respiratory Syndrome Coronavirus: Another Zoonotic Betacoronavirus Causing SARS-Like Disease

(2015) Jasper F. W. Chan et al.   CLINICAL MICROBIOLOGY REVIEWS

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

ViralZone: a knowledge resource to understand virus diversity

(2010) Chantal Hulo et al.   NUCLEIC ACIDS RESEARCH

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery

(2008) Santiago Vilar et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY