De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations

De novo design of new chemical entities for SARS-CoV-2 using artificial intelligence

(2021) Navneet Bung et al.   Future Medicinal Chemistry

De novo design and bioactivity prediction of SARS-CoV-2 main protease inhibitors using recurrent neural network-based transfer learning

(2021) Marcos V. S. Santana et al.   BMC Chemistry

Ongoing COVID-19 Pandemic: A Concise but Updated Comprehensive Review

(2021) Chao Wang et al.   CURRENT MICROBIOLOGY

Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies

(2021) Jianzhong Chen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

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

(2020) Chaolin Huang et al.   LANCET

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

(2020) Abdo A. Elfiky   LIFE SCIENCES

Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs

(2020) Atsushi Hijikata et al.   FEBS LETTERS

Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation

(2020) Shiv Bharadwaj et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds

(2020) Anh-Tien Ton et al.   Molecular Informatics

A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19

(2020) Bin Cao et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Potential Drugs Targeting Early Innate Immune Evasion of SARS-Coronavirus 2 via 2’-O-Methylation of Viral RNA

(2020) José Antonio Encinar et al.   Viruses-Basel

Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

(2020) Mubarak A. Alamri et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach

(2020) Ranabir Majumder et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

(2020) Daniil Polykovskiy et al.   Frontiers in Pharmacology

Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2

(2020) Shafi Mahmud et al.   BRIEFINGS IN BIOINFORMATICS

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

(2019) Jianzhong Chen et al.   NUCLEIC ACIDS RESEARCH

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Advancing Drug Discovery via Artificial Intelligence

(2019) H.C. Stephen Chan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Discovery of Ganoderma lucidum triterpenoids as potential inhibitors against Dengue virus NS2B-NS3 protease

(2019) Shiv Bharadwaj et al.   Scientific Reports

Disulfide bridge formation to increase thermostability of DFPase enzyme: A computational study

(2018) Mozafar Mohammadi et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

Coronaviruses — drug discovery and therapeutic options

(2016) Alimuddin Zumla et al.   NATURE REVIEWS DRUG DISCOVERY

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic

(2010) Tanaji Talele et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY