The art and science of molecular docking

JM Paggi, A Pandit, RO Dror - Annual Review of Biochemistry, 2024 - annualreviews.org
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …

[HTML][HTML] Molecular modeling in drug discovery

TI Adelusi, AQK Oyedele, ID Boyenle… - Informatics in Medicine …, 2022 - Elsevier
With the financial requirements and high time associated with bringing a commercial drug to
the market, the application of computer-aided drug design has been recognized as a …

Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking, and approach with molecular dynamics, RMSD, RMSF, H …

AM da Fonseca, BJ Caluaco, JMC Madureira… - Molecular …, 2024 - Springer
Abstract Severe Acute Respiratory Syndrome caused by a coronavirus is a recent viral
infection. There is no scientific evidence or clinical trials to indicate that possible therapies …

Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships

AAT Naqvi, T Mohammad, GM Hasan… - Current topics in …, 2018 - benthamdirect.com
Protein-ligand interaction is an imperative subject in structure-based drug design and
protein function prediction process. Molecular docking is a computational method which …

[HTML][HTML] Applications of molecular dynamics simulation in protein study

S Sinha, B Tam, SM Wang - Membranes, 2022 - mdpi.com
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study
protein structure-related questions. Starting from the early simulation study on the …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

Enhancing biocatalyst performance through immobilization of lipase (Eversa® Transform 2.0) on hybrid amine-epoxy core-shell magnetic nanoparticles

RLF Melo, TM Freire, RBR Valério, FS Neto… - International Journal of …, 2024 - Elsevier
Magnetic nanoparticles were functionalized with polyethylenimine (PEI) and activated with
epoxy. This support was used to immobilize Lipase (Eversa® Transform 2.0)(EVS) …

[HTML][HTML] The rise of molecular simulations in fragment-based drug design (FBDD): an overview

M Bissaro, M Sturlese, S Moro - Drug Discovery Today, 2020 - Elsevier
Highlights•Fragment-based drug design (FBDD) is revolutionizing the identification and
optimization of new drug candidates.•Molecular simulations-based approaches are …

Computational approaches in drug designing

A Tiwari, S Singh - Bioinformatics, 2022 - Elsevier
Computational approaches are very necessary and useful resources in the process of drug
development. The goal of drug development is to identify a chemical compound that can fit …

Identification of cryptic binding sites using MixMD with standard and accelerated molecular dynamics

RD Smith, HA Carlson - Journal of chemical information and …, 2021 - ACS Publications
Protein dynamics play an important role in small molecule binding and can pose a
significant challenge in the identification of potential binding sites. Cryptic binding sites have …