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 …
Functional protein dynamics directly from sequences
The sequence correlations within a protein multiple sequence alignment are routinely being
used to predict contacts within its structure, but here we point out that these data can also be …
used to predict contacts within its structure, but here we point out that these data can also be …
Characterizing and predicting protein hinges for mechanistic insight
The functioning of proteins requires highly specific dynamics, which depend critically on the
details of how amino acids are packed. Hinge motions are the most common type of large …
details of how amino acids are packed. Hinge motions are the most common type of large …
Comparisons of protein dynamics from experimental structure ensembles, molecular dynamics ensembles, and coarse-grained elastic network models
Predicting protein motions is important for bridging the gap between protein structure and
function. With growing numbers of structures of the same or closely related proteins …
function. With growing numbers of structures of the same or closely related proteins …
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling
W Zheng - Proteins: Structure, Function, and Bioinformatics, 2021 - Wiley Online Library
To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for
small molecules binding in target proteins are in high demand. In this study, we have …
small molecules binding in target proteins are in high demand. In this study, we have …
Equally weighted multiscale elastic network model and its comparison with traditional and parameter-free models
Dynamical properties of proteins play an essential role in their function exertion. The elastic
network model (ENM) is an effective and efficient tool in characterizing the intrinsic …
network model (ENM) is an effective and efficient tool in characterizing the intrinsic …
localpdb—a Python package to manage protein structures and their annotations
J Ludwiczak, A Winski, S Dunin-Horkawicz - Bioinformatics, 2022 - academic.oup.com
Motivation The wealth of protein structures collected in the Protein Data Bank enabled large-
scale studies of their function and evolution. Such studies, however, require the generation …
scale studies of their function and evolution. Such studies, however, require the generation …
Discovery of functional motifs from the interface region of oligomeric proteins using frequent subgraph mining
Modeling the interface region of a protein complex paves the way for understanding its
dynamics and functionalities. Existing works model the interface region of a complex by …
dynamics and functionalities. Existing works model the interface region of a complex by …
Structural database resources for biological macromolecules
LA Abriata - Briefings in bioinformatics, 2017 - academic.oup.com
This Briefing reviews the widely used, currently active, up-to-date databases derived from
the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its …
the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its …
Unveiling Conserved Allosteric Hot Spots in Protein Domains from Sequences
A Hacisuleyman, D Fasshauer - bioRxiv, 2024 - biorxiv.org
The amino acid sequence determines the structure, function, and dynamics of a protein. In
recent years, enormous progress has been made in translating sequence information into …
recent years, enormous progress has been made in translating sequence information into …