One core, two shells: bacterial and eukaryotic ribosomes
S Melnikov, A Ben-Shem… - Nature structural & …, 2012 - nature.com
Ribosomes are universally conserved enzymes that carry out protein biosynthesis. Bacterial
and eukaryotic ribosomes, which share an evolutionarily conserved core, are thought to …
and eukaryotic ribosomes, which share an evolutionarily conserved core, are thought to …
Automated protein function prediction—the genomic challenge
I Friedberg - Briefings in bioinformatics, 2006 - academic.oup.com
Overwhelmed with genomic data, biologists are facing the first big post-genomic question—
what do all genes do? First, not only is the volume of pure sequence and structure data …
what do all genes do? First, not only is the volume of pure sequence and structure data …
Recon3D enables a three-dimensional view of gene variation in human metabolism
Genome-scale network reconstructions have helped uncover the molecular basis of
metabolism. Here we present Recon3D, a computational resource that includes three …
metabolism. Here we present Recon3D, a computational resource that includes three …
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 …
protein domains organised according to their evolutionary and structural relationships. We …
FATCAT 2.0: towards a better understanding of the structural diversity of proteins
Abstract FATCAT 2.0 server (http://fatcat. godziklab. org/), provides access to a flexible
protein structure alignment algorithm developed in our group. In such an alignment …
protein structure alignment algorithm developed in our group. In such an alignment …
Toward the estimation of the absolute quality of individual protein structure models
Motivation: Quality assessment of protein structures is an important part of experimental
structure validation and plays a crucial role in protein structure prediction, where the …
structure validation and plays a crucial role in protein structure prediction, where the …
The structure of the eukaryotic ribosome at 3.0 Å resolution
A Ben-Shem, N Garreau de Loubresse, S Melnikov… - Science, 2011 - science.org
Ribosomes translate genetic information encoded by messenger RNA into proteins. Many
aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are …
aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are …
Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis
Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds
with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and …
with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and …
MMDB and VAST+: tracking structural similarities between macromolecular complexes
T Madej, CJ Lanczycki, D Zhang… - Nucleic acids …, 2014 - academic.oup.com
The computational detection of similarities between protein 3D structures has become an
indispensable tool for the detection of homologous relationships, the classification of protein …
indispensable tool for the detection of homologous relationships, the classification of protein …
The RCSB Protein Data Bank: redesigned web site and web services
Abstract The RCSB Protein Data Bank (RCSB PDB) web site (http://www. pdb. org) has been
redesigned to increase usability and to cater to a larger and more diverse user base. This …
redesigned to increase usability and to cater to a larger and more diverse user base. This …