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 …

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 …

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

L Orellana, O Yoluk, O Carrillo, M Orozco… - Nature …, 2016 - nature.com
Protein conformational changes are at the heart of cell functions, from signalling to ion
transport. However, the transient nature of the intermediates along transition pathways …

Can conformational changes of proteins be represented in torsion angle space? A study with rescaled ridge regression

U Bastolla, Y Dehouck - Journal of Chemical Information and …, 2019 - ACS Publications
Torsion angles are the natural degrees of freedom of protein structures. The ability to
determine torsional variations corresponding to observed changes in Cartesian coordinates …

A stochastic roadmap method to model protein structural transitions

K Molloy, R Clausen, A Shehu - Robotica, 2016 - cambridge.org
Evidence is emerging that the role of protein structure in disease needs to be rethought.
Sequence mutations in proteins are often found to affect the rate at which a protein switches …

Applications of machine learning to problems in biomolecular function and dynamics

R Veevers - 2020 - ueaeprints.uea.ac.uk
Biomolecules such as proteins and nucleic acids are involved in all biological processes. As
they take part in these processes, biomolecules often undergo motions and changes in their …