Classification of intrinsically disordered regions and proteins
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 …
describing protein sequences from a variety of organisms. 1, 2 While this may reflect the …
ConSurf: using evolutionary data to raise testable hypotheses about protein function
Many mutations disappear from the population because they impair protein function and/or
stability. Thus, amino acid positions that are essential for proper function evolve more slowly …
stability. Thus, amino acid positions that are essential for proper function evolve more slowly …
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf
B Yariv, E Yariv, A Kessel, G Masrati, AB Chorin… - Protein …, 2023 - Wiley Online Library
The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and
accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals …
accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals …
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
Abstract IQ-TREE (http://www. iqtree. org, last accessed February 6, 2020) is a user-friendly
and widely used software package for phylogenetic inference using maximum likelihood …
and widely used software package for phylogenetic inference using maximum likelihood …
AlphaFold2 fails to predict protein fold switching
AlphaFold2 has revolutionized protein structure prediction by leveraging sequence
information to rapidly model protein folds with atomic‐level accuracy. Nevertheless, previous …
information to rapidly model protein folds with atomic‐level accuracy. Nevertheless, previous …
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in
DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to …
DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to …
Model selection may not be a mandatory step for phylogeny reconstruction
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …
step in numerous evolutionary studies. Over the years, various criteria for model selection …
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
The mustard family (Brassicaceae) is a scientifically and economically important family,
containing the model plant Arabidopsis thaliana and numerous crop species that feed …
containing the model plant Arabidopsis thaliana and numerous crop species that feed …
PredictProtein—an open resource for online prediction of protein structural and functional features
G Yachdav, E Kloppmann, L Kajan… - Nucleic acids …, 2014 - academic.oup.com
PredictProtein is a meta-service for sequence analysis that has been predicting structural
and functional features of proteins since 1992. Queried with a protein sequence it returns …
and functional features of proteins since 1992. Queried with a protein sequence it returns …
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
It is informative to detect highly conserved positions in proteins and nucleic acid
sequence/structure since they are often indicative of structural and/or functional importance …
sequence/structure since they are often indicative of structural and/or functional importance …