Predicting protein–protein interactions from the molecular to the proteome level
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
ConSurf: using evolutionary data to raise testable hypotheses about protein function
G Celniker, G Nimrod, H Ashkenazy… - Israel Journal of …, 2013 - Wiley Online Library
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 …
CATH: increased structural coverage of functional space
Abstract CATH (https://www. cathdb. info) identifies domains in protein structures from
wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and …
wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and …
[HTML][HTML] Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses
KO Saunders, E Lee, R Parks, DR Martinez, D Li… - Nature, 2021 - nature.com
Betacoronaviruses caused the outbreaks of severe acute respiratory syndrome (SARS) and
Middle East respiratory syndrome, as well as the current pandemic of SARS coronavirus 2 …
Middle East respiratory syndrome, as well as the current pandemic of SARS coronavirus 2 …
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …
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 …
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …
relationships, but this is challenged by the discordant evolution of individual genes. Here we …
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
Deep-learning (DL) methods like DeepMind's AlphaFold2 (AF2) have led to substantial
improvements in protein structure prediction. We analyse confident AF2 models from 21 …
improvements in protein structure prediction. We analyse confident AF2 models from 21 …
CATH: an expanded resource to predict protein function through structure and sequence
The latest version of the CATH-Gene3D protein structure classification database has
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …