Molecular dynamics simulation for all

SA Hollingsworth, RO Dror - Neuron, 2018 - cell.com
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

CHARMM: the biomolecular simulation program

BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Scalable molecular dynamics with NAMD

JC Phillips, R Braun, W Wang… - Journal of …, 2005 - Wiley Online Library
NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

Water determines the structure and dynamics of proteins

MC Bellissent-Funel, A Hassanali, M Havenith… - Chemical …, 2016 - ACS Publications
Water is an essential participant in the stability, structure, dynamics, and function of proteins
and other biomolecules. Thermodynamically, changes in the aqueous environment affect …

Water as an active constituent in cell biology

P Ball - Chemical reviews, 2008 - ACS Publications
When Szent-Györgyi called water the “matrix of life”, 1 he was echoing an old sentiment.
Paracelsus in the 16th century said that “water was the matrix of the world and of all its …

Biomolecular simulation: a computational microscope for molecular biology

RO Dror, RM Dirks, JP Grossman, H Xu… - Annual review of …, 2012 - annualreviews.org
Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Bioinspired super‐wettability from fundamental research to practical applications

L Wen, Y Tian, L Jiang - Angewandte Chemie International …, 2015 - Wiley Online Library
Engineered wettability is a traditional, yet key issue in surface science and attracts
tremendous interest in solving large‐scale practical problems. Recently, different super …

Plant aquaporins: membrane channels with multiple integrated functions

C Maurel, L Verdoucq, DT Luu… - Annu. Rev. Plant Biol., 2008 - annualreviews.org
Aquaporins are channel proteins present in the plasma and intracellular membranes of plant
cells, where they facilitate the transport of water and/or small neutral solutes (urea, boric …

Covalent organic frameworks: pore design and interface engineering

Z Li, T He, Y Gong, D Jiang - Accounts of Chemical Research, 2020 - ACS Publications
Conspectus Nature evolves fascinating molecular pores to achieve unique biological
functions based on a single pore or channel as observed for aquaporins and ion channels …

Aquaporin water channels–from atomic structure to clinical medicine

P Agre, LS King, M Yasui, WB Guggino… - The Journal of …, 2002 - Wiley Online Library
The water permeability of biological membranes has been a longstanding problem in
physiology, but the proteins responsible for this remained unknown until discovery of the …