Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

The Emergence of Omicron: Challenging Times Are Here Again!

(2022) Tanu Singhal   INDIAN JOURNAL OF PEDIATRICS

Omicron BA.2 (B.1.1.529.2): High Potential for Becoming the Next Dominant Variant

(2022) Jiahui Chen et al.   Journal of Physical Chemistry Letters

Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations

(2022) Rahul Singh et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Is Omicron the end of pandemic or start of a new innings?

(2022) Swarnali Das et al.   Travel Medicine and Infectious Disease

ACE-2-Derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2

(2021) Saroj Kumar Panda et al.   JOURNAL OF PROTEOME RESEARCH

Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening

(2021) Madhulata Kumari et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor

(2021) Ahmed A. Al-Karmalawy et al.   Frontiers in Chemistry

A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2

(2021) Rahul Singh et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Chemical system biology approach to identify multi-targeting FDA inhibitors for treating COVID-19 and associated health complications

(2021) Biswajit Naik et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools

(2021) Anish Nag et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Potential of turmeric-derived compounds against RNA‐dependent RNA polymerase of SARS‐CoV‐2: An in-silico approach

(2021) Rahul Singh et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Omicron and Delta variant of SARS‐CoV‐2: A comparative computational study of spike protein

(2021) Suresh Kumar et al.   JOURNAL OF MEDICAL VIROLOGY

Computational Design of Potent D-Peptide Inhibitors of SARS-CoV-2

(2021) Pedro A. Valiente et al.   JOURNAL OF MEDICINAL CHEMISTRY

Covid-19: South Africa’s surge in cases deepens alarm over omicron variant

(2021) Owen Dyer   BMJ-British Medical Journal

Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design

(2021) Nejat Düzgüneş et al.   Pathogens

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

(2020) Roujian Lu et al.   LANCET

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2

(2020) Yanxiao Han et al.   ACS Nano

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

Human Intestinal Defensin 5 Inhibits SARS-CoV-2 Invasion by Cloaking ACE2

(2020) Cheng Wang et al.   GASTROENTEROLOGY

A human neutralizing antibody targets the receptor binding site of SARS-CoV-2

(2020) Rui Shi et al.   NATURE

Human neutralizing antibodies elicited by SARS-CoV-2 infection

(2020) Bin Ju et al.   NATURE

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

The HDOCK server for integrated protein–protein docking

(2020) Yumeng Yan et al.   Nature Protocols

Rare driver mutations in head and neck squamous cell carcinomas converge on NOTCH signaling

(2020) Sampath K. Loganathan et al.   SCIENCE

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

The genetic sequence, origin, and diagnosis of SARS-CoV-2

(2020) Huihui Wang et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells

(2020) Mirza S. Baig et al.   DRUGS IN R&D

Angiotensin-converting enzyme 2 (ACE2) receptor and SARS-CoV-2: Potential therapeutic targeting

(2020) Sourena Sharifkashani et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment

(2020) Biswajit Naik et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors

(2020) Hemlata Pundir et al.   MOLECULAR DIVERSITY

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding

(2020) James R. Byrnes et al.   mSphere

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

(2020) Desiree Schütz et al.   ADVANCED DRUG DELIVERY REVIEWS

Cholesterol-lowering drugs the simvastatin and atorvastatin change the protease activity of pepsin: An experimental and computational study

(2020) Mohsen Shahlaei et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

HIV-1 anchor inhibitors and membrane fusion inhibitors target distinct but overlapping steps in virus entry

(2019) Dirk Eggink et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Comprehensive Review on Current Advances in Peptide Drug Development and Design

(2019) Andy Chi-Lung Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Antiviral peptides as promising therapeutic drugs

(2019) Liana Costa Pereira Vilas Boas et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Precision medicine by designer interference peptides: applications in oncology and molecular therapeutics

(2019) Anabel Sorolla et al.   ONCOGENE

Therapeutic peptides: Historical perspectives, current development trends, and future directions

(2018) Jolene L. Lau et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review

(2018) Zhifeng Liu et al.   CHEMOSPHERE

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Antimicrobial Peptides

(2018) Donald E. Fry   Surgical Infections

Atomistic details on the mechanism of organophosphates resistance in insects: Insights from homology modeling, docking and molecular dynamic simulation

(2018) Sajad Moradi et al.   JOURNAL OF MOLECULAR LIQUIDS

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

(2017) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking

(2017) Yumeng Yan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exploring dual inhibitory role of febrifugine analogues againstPlasmodiumutilizing structure-based virtual screening and molecular dynamic simulation

(2016) Rajan Kumar Pandey et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

First-in-human application of the novel hepatitis B and hepatitis D virus entry inhibitor myrcludex B

(2016) Antje Blank et al.   JOURNAL OF HEPATOLOGY

Regulation of protein-ligand binding affinity by hydrogen bond pairing

(2016) D. Chen et al.   Science Advances

EPI-X4, a novel endogenous antagonist of CXCR4

(2015) Christian Buske et al.   Oncotarget

Protease Inhibitors from Marine Actinobacteria as a Potential Source for Antimalarial Compound

(2014) L. Karthik et al.   PLoS One

Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study

(2014) Hemanth Naick Banavath et al.   Scientific Reports

AllergenFP: allergenicity prediction by descriptor fingerprints

(2013) I. Dimitrov et al.   BIOINFORMATICS

AllerTOP - a server for in silico prediction of allergens

(2013) Ivan Dimitrov et al.   BMC BIOINFORMATICS

Future directions for peptide therapeutics development

(2013) Allan A. Kaspar et al.   DRUG DISCOVERY TODAY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Antiviral Mechanisms of Human Defensins

(2013) Sarah S. Wilson et al.   JOURNAL OF MOLECULAR BIOLOGY

AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses

(2013) Abid Qureshi et al.   NUCLEIC ACIDS RESEARCH

HIPdb: A Database of Experimentally Validated HIV Inhibiting Peptides

(2013) Abid Qureshi et al.   PLoS One

A Rationally Engineered Anti-HIV Peptide Fusion Inhibitor with Greatly Reduced Immunogenicity

(2012) F. Brauer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

Screening and Rational Design of Hepatitis C Virus Entry Inhibitory Peptides Derived from GB Virus A NS5A

(2012) Xiuying Liu et al.   JOURNAL OF VIROLOGY

Antimicrobial peptides important in innate immunity

(2011) Andreas Cederlund et al.   FEBS Journal

Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding

(2011) Joseph A. Marsh et al.   STRUCTURE

Association between nasal shedding and fever that influenza A (H3N2) induces in dogs

(2011) Daesub Song et al.   Virology Journal

Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency

(2010) Han Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Small Peptide Inhibitors Disrupt a High-Affinity Interaction between Cytoplasmic Dynein and a Viral Cargo Protein

(2010) Bruno Hernáez et al.   JOURNAL OF VIROLOGY

Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides

(2010) Joshua M. Costin et al.   PLoS Neglected Tropical Diseases

Fine Mapping of Pre-S Sequence Requirements for Hepatitis B Virus Large Envelope Protein-Mediated Receptor Interaction

(2009) A. Schulze et al.   JOURNAL OF VIROLOGY

Radius of gyration as an indicator of protein structure compactness

(2008) M. Yu. Lobanov et al.   MOLECULAR BIOLOGY