Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
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 …
Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments
C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …
that protein function can be accompanied or assisted by structural fluctuations and …
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 …
In Silico Strategies in Tuberculosis Drug Discovery
Tuberculosis (TB) remains a serious threat to global public health, responsible for an
estimated 1.5 million mortalities in 2018. While there are available therapeutics for this …
estimated 1.5 million mortalities in 2018. While there are available therapeutics for this …
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations
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 …
transport. However, the transient nature of the intermediates along transition pathways …
CABS-flex predictions of protein flexibility compared with NMR ensembles
Motivation: Identification of flexible regions of protein structures is important for
understanding of their biological functions. Recently, we have developed a fast approach for …
understanding of their biological functions. Recently, we have developed a fast approach for …
Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope
L Orellana, AH Thorne, R Lema… - Proceedings of the …, 2019 - National Acad Sciences
Epidermal growth factor receptor (EGFR) signaling is initiated by a large ligand-favored
conformational change of the extracellular domain (ECD) from a closed, self-inhibited …
conformational change of the extracellular domain (ECD) from a closed, self-inhibited …
Residues coevolution guides the systematic identification of alternative functional conformations in proteins
P Sfriso, M Duran-Frigola, R Mosca, A Emperador… - Structure, 2016 - cell.com
We present here a new approach for the systematic identification of functionally relevant
conformations in proteins. Our fully automated pipeline, based on discrete molecular …
conformations in proteins. Our fully automated pipeline, based on discrete molecular …
[HTML][HTML] Thermodynamics and folding landscapes of large proteins from a statistical mechanical model
Statistical mechanical models that afford an intermediate resolution between macroscopic
chemical models and all-atom simulations have been successful in capturing folding …
chemical models and all-atom simulations have been successful in capturing folding …