Molecular dynamics simulations: advances and applications
Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …
effectively to understand macromolecular structure-to-function relationships. Present …
The role of protein loops and linkers in conformational dynamics and allostery
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …
take place on a wide range of time scales. These changes can be as small as the rotation of …
[图书][B] Coarse-graining of condensed phase and biomolecular systems
GA Voth - 2008 - taylorfrancis.com
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …
Biomolecular Systems examines systematic ways of constructing coarse-grained …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier
L Orellana - Frontiers in molecular biosciences, 2019 - frontiersin.org
Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …
function at the cell and organism scale, but have been elusive both experimentally and …
Protein structure fitting and refinement guided by cryo-EM density
For many macromolecular assemblies, both a cryo-electron microscopy map and atomic
structures of its component proteins are available. Here we describe a method for fitting and …
structures of its component proteins are available. Here we describe a method for fitting and …
iMod: multipurpose normal mode analysis in internal coordinates
Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …
are critical for understanding macromolecular functioning. Coarse-grained representations …
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms
Allostery, the coupling between ligand binding and protein conformational change, is the
heart of biological network and it has often been explained by two representative models …
heart of biological network and it has often been explained by two representative models …
A database of macromolecular motions
M Gerstein, W Krebs - Nucleic acids research, 1998 - academic.oup.com
We describe a database of macromolecular motions meant to be of general use to the
structural community. the database, which is accessible on the world wide web with an entry …
structural community. the database, which is accessible on the world wide web with an entry …
A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export
Superfamily 1 and superfamily 2 RNA helicases are ubiquitous messenger-RNA–protein
complex (mRNP) remodelling enzymes that have critical roles in all aspects of RNA …
complex (mRNP) remodelling enzymes that have critical roles in all aspects of RNA …