Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Intrinsically disordered proteins and their “mysterious”(meta) physics

VN Uversky - Frontiers in Physics, 2019 - frontiersin.org
Recognition of the natural abundance and functional importance of intrinsically disordered
proteins (IDPs), and protein hybrids that contain both intrinsically disordered protein regions …

Intrinsically disordered proteins: an overview

R Trivedi, HA Nagarajaram - International journal of molecular sciences, 2022 - mdpi.com
Many proteins and protein segments cannot attain a single stable three-dimensional
structure under physiological conditions; instead, they adopt multiple interconverting …

Stress-triggered phase separation is an adaptive, evolutionarily tuned response

JA Riback, CD Katanski, JL Kear-Scott, EV Pilipenko… - Cell, 2017 - cell.com
In eukaryotic cells, diverse stresses trigger coalescence of RNA-binding proteins into stress
granules. In vitro, stress-granule-associated proteins can demix to form liquids, hydrogels …

De novo engineering of intracellular condensates using artificial disordered proteins

M Dzuricky, BA Rogers, A Shahid, PS Cremer… - Nature …, 2020 - nature.com
Phase separation of intrinsically disordered proteins (IDPs) is a remarkable feature of living
cells to dynamically control intracellular partitioning. Despite the numerous new IDPs that …

Intrinsically disordered proteins in cellular signalling and regulation

PE Wright, HJ Dyson - Nature reviews Molecular cell biology, 2015 - nature.com
Intrinsically disordered proteins (IDPs) are important components of the cellular signalling
machinery, allowing the same polypeptide to undertake different interactions with different …

Classification of intrinsically disordered regions and proteins

R Van Der Lee, M Buljan, B Lang, RJ Weatheritt… - Chemical …, 2014 - ACS Publications
Over the past decade, we have observed a massive increase in the amount of information
describing protein sequences from a variety of organisms. 1, 2 While this may reflect the …

Continuous distributed representation of biological sequences for deep proteomics and genomics

E Asgari, MRK Mofrad - PloS one, 2015 - journals.plos.org
We introduce a new representation and feature extraction method for biological sequences.
Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors …

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

DT Jones, D Cozzetto - Bioinformatics, 2015 - academic.oup.com
Motivation: A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions
(IDRs), which act in unfolded states or by undergoing transitions between structured and …

[HTML][HTML] CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins

AS Holehouse, RK Das, JN Ahad, MOG Richardson… - Biophysical journal, 2017 - cell.com
Intrinsically disordered proteins and regions (IDPs) represent a large class of proteins that
are defined by conformational heterogeneity and lack of persistent tertiary/secondary …