The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

S Wan, AP Bhati, DW Wright, AD Wade, G Tresadern… - Scientific Reports, 2022 - nature.com
Optimization of binding affinities for compounds to their target protein is a primary objective
in drug discovery. Herein we report on a collaborative study that evaluates a set of …

[HTML][HTML] Contribution of Nischarin/IRAS in CNS development, injury and diseases

P Zheng, C Pan, C Zhou, B Liu, L Wang, S Duan… - Journal of Advanced …, 2023 - Elsevier
Abstract Background Murine Nischarin and its human homolog IRAS are scaffold proteins
highly expressed in the central nervous system (CNS). Nischarin was initially discovered as …

General theory of specific binding: insights from a genetic-mechano-chemical protein model

JM McBride, JP Eckmann, T Tlusty - Molecular Biology and …, 2022 - academic.oup.com
Proteins need to selectively interact with specific targets among a multitude of similar
molecules in the cell. However, despite a firm physical understanding of binding …

[HTML][HTML] Computational design of novel therapeutics targeting Schistosomiasis, a neglected tropical disease

MT Ibrahim, SC Ja'afaru, A Uzairu, A Chandra… - Scientific African, 2024 - Elsevier
Schistosomiasis, caused by flatworm parasites, is a widespread disease resulting in chronic
illness and fatalities globally. Given the risk of drug resistance and limited treatment options …

Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations

P Wang, X Gao, K Zhang, Q Pei, X Xu, F Yan… - Physical Chemistry …, 2021 - pubs.rsc.org
Positive allosteric modulators (PAMs) of human metabotropic glutamate receptor 2 (hmGlu2)
are well-known in the treatment of psychiatric disorders for their higher selectivity and lower …

Structure‐based computational design of antibody mimetics: challenges and perspectives

EJF Chaves, DF Coêlho, CHB Cruz… - FEBS Open …, 2024 - Wiley Online Library
The design of antibody mimetics holds great promise for revolutionizing therapeutic
interventions by offering alternatives to conventional antibody therapies. Structure‐based …

The physical logic of protein machines

JM McBride, T Tlusty - Journal of Statistical Mechanics: Theory …, 2024 - iopscience.iop.org
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of
the amino acid building blocks and their dynamic network of many-body interactions. These …

In silico Exploration of Dakshina Kannada Medicinal Plants as Anti-SARS-CoV-2 Agents by Molecular Docking and Simulation Approaches

JP James, D Jyothi, V Devaraji… - Letters in Drug Design & …, 2023 - ingentaconnect.com
Aims: The rich ethnomedicinal practices of Dakshina Kannada have received considerable
attention, and many treatment methods have been documented. This work aimed to explore …

[PDF][PDF] Computer Aided Drug Discovery Utilization in Conservative Dentistry

AE Prahasti, T Yuanita, RP Rahayu - Journal of International Dental and …, 2022 - jidmr.com
Computer aided drugs discovery or in silico design is bioinformatics' contribution that
supports pharmacy, medical and dentistry fields. It creates innovation in the search, design …

Computational methods for molecular understanding of the antibiotic‐aminoacyl tRNA synthetase interaction

S Chowdhury, P Ghosh, N Nandi - Current Protocols, 2023 - Wiley Online Library
Developing an understanding of the interactions between an antibiotic and its binding site in
a pathogen cell is the key to antibiotic design—an important cost‐saving methodology …