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 …

The plant invertase/pectin methylesterase inhibitor superfamily

D Coculo, V Lionetti - Frontiers in plant science, 2022 - frontiersin.org
Invertases (INVs) and pectin methylesterases (PMEs) are essential enzymes coordinating
carbohydrate metabolism, stress responses, and sugar signaling. INVs catalyzes the …

GeneMANIA update 2018

M Franz, H Rodriguez, C Lopes, K Zuberi… - Nucleic acids …, 2018 - academic.oup.com
Abstract GeneMANIA (http://genemania. org) is a flexible user-friendly web site for
generating hypotheses about gene function, analyzing gene lists and prioritizing genes for …

Phase separation of a yeast prion protein promotes cellular fitness

TM Franzmann, M Jahnel, A Pozniakovsky, J Mahamid… - Science, 2018 - science.org
INTRODUCTION The formation of dynamic, membraneless compartments using intracellular
phase transitions such as phase separation and gelation provides an efficient way for cells …

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

A Andreeva, E Kulesha, J Gough… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Structural Classification of Proteins (SCOP) database is a classification of
protein domains organised according to their evolutionary and structural relationships. We …

Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei

K Billington, C Halliday, R Madden, P Dyer… - Nature …, 2023 - nature.com
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and
plant unicellular parasites. Understanding their complex cell architecture and life cycle is …

The Ensembl gene annotation system

BL Aken, S Ayling, D Barrell, L Clarke, V Curwen… - Database, 2016 - academic.oup.com
The Ensembl gene annotation system has been used to annotate over 70 different
vertebrate species across a wide range of genome projects. Furthermore, it generates the …

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

T Mock, RP Otillar, J Strauss, M McMullan, P Paajanen… - Nature, 2017 - nature.com
Abstract The Southern Ocean houses a diverse and productive community of organisms,.
Unicellular eukaryotic diatoms are the main primary producers in this environment, where …

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

HA Shihab, J Gough, DN Cooper, PD Stenson… - Human …, 2013 - Wiley Online Library
The rate at which nonsynonymous single nucleotide polymorphisms (ns SNP s) are being
identified in the human genome is increasing dramatically owing to advances in whole …

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

NK Fox, SE Brenner, JM Chandonia - Nucleic acids research, 2014 - academic.oup.com
Abstract Structural Classification of Proteins—extended (SCOPe, http://scop. berkeley. edu)
is a database of protein structural relationships that extends the SCOP database. SCOP is a …