Relative binding free energy calculations in drug discovery: recent advances and practical considerations

Z Cournia, B Allen, W Sherman - Journal of chemical information …, 2017‏ - ACS Publications
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states

E Brunk, U Rothlisberger - Chemical reviews, 2015‏ - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …

Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design

PG Francoeur, T Masuda, J Sunseri, A Jia… - Journal of chemical …, 2020‏ - ACS Publications
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …

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 …

Docking and scoring in virtual screening for drug discovery: methods and applications

DB Kitchen, H Decornez, JR Furr… - Nature reviews Drug …, 2004‏ - nature.com
Computational approaches that'dock'small molecules into the structures of macromolecular
targets and'score'their potential complementarity to binding sites are widely used in hit …

Molecular dynamics simulations of biomolecules

M Karplus, JA McCammon - Nature structural biology, 2002‏ - nature.com
Molecular dynamics simulations are important tools for understanding the physical basis of
the structure and function of biological macromolecules. The early view of proteins as …

The many roles of computation in drug discovery

WL Jorgensen - Science, 2004‏ - science.org
The Many Roles of Computation in Drug Discovery | Science Skip to main content news
careers commentary Journals Science Log in Become A Member journal-menu-img science …

Molecular dynamics: survey of methods for simulating the activity of proteins

SA Adcock, JA McCammon - Chemical reviews, 2006‏ - ACS Publications
The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

S Wan, AP Bhati, SJ Zasada… - Interface focus, 2020‏ - royalsocietypublishing.org
A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

IS Moreira, PA Fernandes… - … : Structure, Function, and …, 2007‏ - Wiley Online Library
Proteins tendency to bind to one another in a highly specific manner forming stable
complexes is fundamental to all biological processes. A better understanding of complex …