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 …

Using Xplor–NIH for NMR molecular structure determination

CD Schwieters, JJ Kuszewski, GM Clore - Progress in nuclear magnetic …, 2006 - Elsevier
Xplor–NIH [1] is a generalized package for biomolecular structure determination from
experimental NMR data combined with known geometric data. This is achieved by seeking …

Global analysis of protein folding using massively parallel design, synthesis, and testing

GJ Rocklin, TM Chidyausiku, I Goreshnik, A Ford… - Science, 2017 - science.org
Proteins fold into unique native structures stabilized by thousands of weak interactions that
collectively overcome the entropic cost of folding. Although these forces are “encoded” in the …

Accurate de novo design of hyperstable constrained peptides

G Bhardwaj, VK Mulligan, CD Bahl, JM Gilmore… - Nature, 2016 - nature.com
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks
generally have shapes that have evolved to fit precisely into binding pockets on their targets …

Principles for designing ideal protein structures

N Koga, R Tatsumi-Koga, G Liu, R **, M Habeck, B Bardiaux, A Bernard… - …, 2007 - academic.oup.com
Modern structural genomics projects demand for integrated methods for the interpretation
and storage of nuclear magnetic resonance (NMR) data. Here we present version 2.1 of our …

Mechanism for the activation of the anaplastic lymphoma kinase receptor

AV Reshetnyak, P Rossi, AG Myasnikov, M Sowaileh… - Nature, 2021 - nature.com
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase (RTK) that regulates
important functions in the central nervous system,. The ALK gene is a hotspot for …

Recognition and specificity determinants of the human cbx chromodomains

L Kaustov, H Ouyang, M Amaya, A Lemak… - Journal of Biological …, 2011 - ASBMB
The eight mammalian Cbx proteins are chromodomain-containing proteins involved in
regulation of heterochromatin, gene expression, and developmental programs. They are …