4.7 Article

Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking

Related references

Note: Only part of the references are listed.
Letter Gastroenterology & Hepatology

Global prediction of primary liver cancer incidences and mortality in 2040

Chenxi Li et al.

JOURNAL OF HEPATOLOGY (2023)

Article Biochemistry & Molecular Biology

Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation

Adnane Aouidate et al.

Summary: The new SARS-CoV-2 coronavirus has caused the COVID-19 pandemic, with no effective treatments or vaccines available currently. Computational methods have been used to identify potential virus inhibitors, leading to the discovery of three promising compounds for fighting COVID-19. Molecular dynamics simulations showed that these compounds remained stable and may be suitable candidates for further experimental analysis.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Chemistry, Medicinal

Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database

Jurica Novak et al.

Summary: Through virtual screening and molecular dynamics simulations, this study identified eight molecules with potential inhibitory properties, possessing appropriate ADMET characteristics. The study demonstrates that these ligands can bind not only at the catalytic site of the enzyme, but also at crucial binding sites.

FUTURE MEDICINAL CHEMISTRY (2021)

Article Chemistry, Medicinal

Complementarity principle in terms of electron density for the study of EGFR complexes

Shivananda Kandagalla et al.

Summary: The complementarity principle is a well-established concept in chemistry and biology, where the overlap of electron clouds can be used to determine the complementarity of intermolecular contacts. In this study, a mathematical relation between the overlap of ligand and enzyme electron clouds was examined for 64 EGFR-ligand complexes, showing a high correlation between the overlap and calculated terms. This provides a strong basis for bioactivity prognosis and molecular docking studies.

FUTURE MEDICINAL CHEMISTRY (2021)

Article Chemistry, Medicinal

Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses

Hrvoje Rimac et al.

Summary: In this article, the AlteQ method is proposed for evaluating the correctness of ligand binding poses, calculating the electron density between the ligand and receptor, bypassing the drawbacks of using ligand RMSD, and improving the fraction of recovered ligand-receptor contacts method. Free versions of the AlteQ program for assessing complementarity between the ligand and receptor are available for download.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Medicinal

Identification of Zika Virus NS2B-NS3 Protease Inhibitors by Structure-Based Virtual Screening and Drug Repurposing Approaches

Felipe R. S. Santos et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Multidisciplinary Sciences

Zika Virus NS3 Protease Pharmacophore Anchor Model and Drug Discovery

Nikhil Pathak et al.

Scientific Reports (2020)

Article Chemistry, Medicinal

Electron density analysis of CDK complexes using the AlteQ method

Hrvoje Rimac et al.

FUTURE MEDICINAL CHEMISTRY (2020)

Review Chemistry, Multidisciplinary

A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Tamer N. Jarada et al.

JOURNAL OF CHEMINFORMATICS (2020)

Article Biochemical Research Methods

Computational insights into the binding mode of curcumin analogues against EP300 HAT domain as potent acetyltransferase inhibitors

Shivananda Kandagalla et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2020)

Article Chemistry, Multidisciplinary

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

Jeffrey A. van Santen et al.

ACS CENTRAL SCIENCE (2019)

Article Biochemistry & Molecular Biology

PubChem 2019 update: improved access to chemical data

Sunghwan Kim et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Biotechnology & Applied Microbiology

Drug repurposing: progress, challenges and recommendations

Sudeep Pushpakom et al.

NATURE REVIEWS DRUG DISCOVERY (2019)

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biology

Cysteine proteases secreted by the pinewood nematode, Bursaphelenchus xylophilus: In silico analysis

Joana M. S. Cardoso et al.

COMPUTATIONAL BIOLOGY AND CHEMISTRY (2018)

Review Immunology

Clinical & epidemiological significance of Kyasanur forest disease

Ashok Munivenkatappa et al.

INDIAN JOURNAL OF MEDICAL RESEARCH (2018)

Review Biochemistry & Molecular Biology

Zika Virus Protease: An Antiviral Drug Target

CongBao Kang et al.

TRENDS IN MICROBIOLOGY (2017)

Article Multidisciplinary Sciences

Repurposing of the anti-malaria drug chloroquine for Zika Virus treatment and prophylaxis

Sergey A. Shiryaev et al.

SCIENTIFIC REPORTS (2017)

Article Biochemical Research Methods

Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection

Nikhil Pathak et al.

BMC BIOINFORMATICS (2017)

Article Chemistry, Medicinal

Flavivirus NS2B/NS3 Protease: Structure, Function, and Inhibition

Zhong Li et al.

VIRAL PROTEASES AND THEIR INHIBITORS (2017)

Review Pharmacology & Pharmacy

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Samuel Genheden et al.

EXPERT OPINION ON DRUG DISCOVERY (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Medicinal

An Aggregation Advisor for Ligand Discovery

John J. Irwin et al.

JOURNAL OF MEDICINAL CHEMISTRY (2015)

Review Pharmacology & Pharmacy

Beware of docking!

Yu-Chian Chen

TRENDS IN PHARMACOLOGICAL SCIENCES (2015)

Article Infectious Diseases

On the transmission pattern of Kyasanur Forest disease (KFD) in India

Manoj V. Murhekar et al.

INFECTIOUS DISEASES OF POVERTY (2015)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Infectious Diseases

Coverage and Effectiveness of Kyasanur Forest Disease (KFD) Vaccine in Karnataka, South India, 2005-10

Gudadappa S. Kasabi et al.

PLOS NEGLECTED TROPICAL DISEASES (2013)

Review Pharmacology & Pharmacy

Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives

V. K. Vyas et al.

INDIAN JOURNAL OF PHARMACEUTICAL SCIENCES (2012)

Article Chemistry, Medicinal

Combining Global and Local Measures for Structure-Based Druggability Predictions

Andrea Volkamer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Physical

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

Bill R. Miller et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Microbiology

2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase

Hongping Dong et al.

PLOS PATHOGENS (2012)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

QMEAN server for protein model quality estimation

Pascal Benkert et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Virology

Role of nonstructural protein NS2A in flavivirus assembly

Jason Y. Leung et al.

JOURNAL OF VIROLOGY (2008)

Article Biochemistry & Molecular Biology

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Markus Wiederstein et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Article Biotechnology & Applied Microbiology

Dengue virus NS4B interacts with NS3 and dissociates it from single-stranded RNA

Indira Umareddy et al.

JOURNAL OF GENERAL VIROLOGY (2006)

Article Biochemistry & Molecular Biology

FAF-Drugs: free ADME/tox filtering of compound collections

Maria A. Miteva et al.

NUCLEIC ACIDS RESEARCH (2006)

Review Virology

Kyasanur forest diseasea: an epidemiological view in India

Priyabrata Pattnaik

REVIEWS IN MEDICAL VIROLOGY (2006)

Article Virology

Inhibition of alpha/beta interferon signaling by the NS4B protein of flaviviruses

JL Muñoz-Jordán et al.

JOURNAL OF VIROLOGY (2005)

Article Biotechnology & Applied Microbiology

Drug repositioning: Identifying and developing new uses for existing drugs

TT Ashburn et al.

NATURE REVIEWS DRUG DISCOVERY (2004)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Review Chemistry, Multidisciplinary

Serine protease mechanism and specificity

L Hedstrom

CHEMICAL REVIEWS (2002)

Article Biochemistry & Molecular Biology

Completeness in structural genomics

D Vitkup et al.

NATURE STRUCTURAL BIOLOGY (2001)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)