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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology. Expand
Up-to-date catalogues of yeast protein complexes
Two catalogues of yeast protein complexes are reported, one of which is a comprehensive catalogue of 408 manually curated heteromeric protein complexes reliably backed by small-scale experiments reported in the current literature and the other comprises 400 high-throughput complexes annotated with current literature evidence. Expand
SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.
In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and forExpand
A Census of Human Soluble Protein Complexes
Whereas larger multiprotein assemblies tend to be more extensively annotated and evolutionarily conserved, human protein complexes with five or fewer subunits are far more likely to be functionally unannotated or restricted to vertebrates, suggesting more recent functional innovations. Expand
Deviations from standard atomic volumes as a quality measure for protein crystal structures.
Atomic volumes, themselves not directly restrained in crystallographic refinement, can provide an independent, rather sensitive, measure of the quality of a protein structure, and it is found that the Z-score rms decreases as the resolution and R-factor improve, consistent with the fact that these improvements generally reflect more accurate models. Expand
CYGD: the Comprehensive Yeast Genome Database
The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen asExpand
CAPRI: A Critical Assessment of PRedicted Interactions
The motivations for launching CAPRI, the rules that were applied to select targets and run the experiment, the results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems, and some conclusions can already be drawn. Expand
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first major evaluation of blind predictions, which reveals genuine progress but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility. Expand
ACLAME: A CLAssification of Mobile genetic Elements
The ACLAME database is a collection and classification of prokaryotic mobile genetic elements from various sources, comprising all known phage genomes, plasmids and transposons, and aims to build a comprehensive classification of the functional modules of MGEs at the protein, gene and higher levels. Expand
The TXP Motif in the Second Transmembrane Helix of CCR5
A sequence motif (TXP) in the second transmembrane helix of chemokine receptors was identified and its role was investigated by theoretical and experimental approaches and the functional response was found to depend strongly on the nature of the substituted side chain. Expand