Molecular dynamics simulation of the interaction of food proteins with small molecules

X Hu, Z Zeng, J Zhang, D Wu, H Li, F Geng - Food Chemistry, 2023 - Elsevier
Molecular dynamics (MD) simulation is used increasingly to explore mechanisms of
interactions and conformational relationships between food proteins and other food …

Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview

V Salmaso, S Moro - Frontiers in pharmacology, 2018 - frontiersin.org
Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …

AI-based protein structure prediction in drug discovery: impacts and challenges

M Schauperl, RA Denny - Journal of Chemical Information and …, 2022 - ACS Publications
Proteins are the molecular machinery of the human body, and their malfunctioning is often
responsible for diseases, making them crucial targets for drug discovery. The three …

A brief history of bioinformatics

J Gauthier, AT Vincent, SJ Charette… - Briefings in …, 2019 - academic.oup.com
It is easy for today's students and researchers to believe that modern bioinformatics
emerged recently to assist next-generation sequencing data analysis. However, the very …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Toward the solution of the protein structure prediction problem

R Pearce, Y Zhang - Journal of Biological Chemistry, 2021 - ASBMB
Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

S Pronk, S Páll, R Schulz, P Larsson, P Bjelkmar… - …, 2013 - academic.oup.com
Motivation: Molecular simulation has historically been a low-throughput technique, but faster
computers and increasing amounts of genomic and structural data are changing this by …

A multi-analytical approach to peer-to-peer mobile payment acceptance prediction

Z Kalinic, V Marinkovic, S Molinillo… - Journal of Retailing and …, 2019 - Elsevier
This research is a pioneering study into peer-to-peer mobile payment (P2PM-pay) systems'
adoption. It proposes a behavioral model of the use of P2PM-pay systems and identifies the …

Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born

AW Gotz, MJ Williamson, D Xu, D Poole… - Journal of chemical …, 2012 - ACS Publications
We present an implementation of generalized Born implicit solvent all-atom classical
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …

Generalized Born implicit solvent models for biomolecules

AV Onufriev, DA Case - Annual review of biophysics, 2019 - annualreviews.org
It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …