Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
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 …

Liquid–liquid phase separation by intrinsically disordered protein regions of viruses: Roles in viral life cycle and control of virus–host interactions

S Brocca, R Grandori, S Longhi, V Uversky - International Journal of …, 2020 - mdpi.com
Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under
physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs …

flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

G Hu, A Katuwawala, K Wang, Z Wu… - Nature …, 2021 - nature.com
Identification of intrinsic disorder in proteins relies in large part on computational predictors,
which demands that their accuracy should be high. Since intrinsic disorder carries out a …

[HTML][HTML] Transcription factors activate genes through the phase-separation capacity of their activation domains

A Boija, IA Klein, BR Sabari, A Dall'Agnese, EL Coffey… - Cell, 2018 - cell.com
Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding
domains (DBDs) and activation domains (ADs). The DBDs have been well characterized …

Extreme disorder in an ultrahigh-affinity protein complex

A Borgia, MB Borgia, K Bugge, VM Kissling… - Nature, 2018 - nature.com
Molecular communication in biology is mediated by protein interactions. According to the
current paradigm, the specificity and affinity required for these interactions are encoded in …

Intrinsically disordered regions direct transcription factor in vivo binding specificity

S Brodsky, T Jana, K Mittelman, M Chapal, DK Kumar… - Molecular cell, 2020 - cell.com
Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …

Rapid prediction and analysis of protein intrinsic disorder

GW Dayhoff, VN Uversky - Protein Science, 2022 - Wiley Online Library
Protein intrinsic disorder is found in all kingdoms of life and is known to underpin numerous
physiological and pathological processes. Computational methods play an important role in …

Protein structure and function prediction using I‐TASSER

J Yang, Y Zhang - Current protocols in bioinformatics, 2015 - Wiley Online Library
I‐TASSER is a hierarchical protocol for automated protein structure prediction and structure‐
based function annotation. Starting from the amino acid sequence of target proteins, I …

Alpha-synuclein aggregation pathway in Parkinson's disease: current status and novel therapeutic approaches

M Vidović, MG Rikalovic - Cells, 2022 - mdpi.com
Following Alzheimer's, Parkinson's disease (PD) is the second-most common
neurodegenerative disorder, sharing an unclear pathophysiology, a multifactorial profile …

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

FG Quiroz, A Chilkoti - Nature materials, 2015 - nature.com
Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-
assembly in nature and in man-made material systems. Yet little is known about how the …