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RCSB PDB / The Research Collaboratory for Structural Bioinformatics Protein Data Bank
Helps students and researchers to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. RCSB PDB is a database that provides a resource powered by the Protein Data Bank (PDB) archive - information about the 3D shapes of proteins, nucleic acids, and complex assemblies. Users can perform simple and complex queries on the data, analyze, and visualize the results.
HSSP / Homology-derived Secondary Structure of Proteins
New
Consists of a derived database merging information from three-dimensional structures and one-dimensional sequences of proteins. HSSP is a resource of aligned sequence families, but also a database of implied secondary and tertiary structures. It can be useful for analyzing residue conservation in structural context, for defining structurally meaningful sequence patterns and, in general, for studying protein evolution, folding and design.
Proteopedia
Stores 3D structures of proteins and other molecules, with descriptive text and hyperlinks that change the adjacently displayed structures to coincide with points made in the text. Proteopedia is a wiki-based web-resource for all scientists who need to utilize three-dimensional (3D) structural information in their research, and for educators requiring a medium for compelling presentation of structure-function relationships. 3D scenes of molecules and molecular complexes can be created easily by Proteopedia users and immediately shared with and viewed by all.
DomIns
Provides information on domain insertions in known protein structures. DomIns is a web resource using the Structural Classification of Proteins (SCOP) protein domain definitions to identify insertions. It allows user to search by (i) Protein Data Bank (PDB) or SCOP identifier, (ii) keywords, (iii) browsing all insertions, (iv) by insertion type or (v) by SCOP class combination. The database can be used to undertake studies on the effect of domain insertions on protein folding and to expand the repertoire of multifunctional hybrid proteins.
BEGDB / Benchmark Energy and Geometry DataBase
Collects results of highly accurate QM (quantum mechanics) calculations of molecular structures, energies and properties. BEGDB hosts data which can serve as benchmarks for testing and parameterization of other computational methods. In BEGDB, data are organized into datasets that contain the result from separate publications. More details, including full citation and link to the original paper are accessible from the listing of the datasets using the Details link. All the data displayed in the results table can be downloaded in comma-separated values (CSV) format and geometries of the molecules/systems can be downloaded as a single zip archive.
CAMEO / Continuous Automated Model EvaluatiOn
Evaluates the accuracy and reliability of protein structures, ligand binding sites and quality models predictions. CAMEO is a community project that works in a fully automated manner. This project supports both the developers of structure prediction servers as well as the users of theoretical models. CAMEO is an open platform, applying assessment criteria established by the protein structure prediction community, and implementing new assessment categories on demand.
LiveBench
Obsolete
Is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods. LiveBench focuses mainly on homology modeling and protein threading but also includes secondary structure prediction, comparing publicly available webserver output to newly deposited protein structures in the Protein Data Bank (PDB). Like the EVA project and unlike the related CASP and CAFASP experiments, LiveBench is intended to study the accuracy of predictions that would be obtained by non-expert users of publicly available prediction methods. A major advantage of LiveBench and EVA over CASP projects, which run once every two years is their comparatively large data set.
ISSD / Integrated Sequence-Structure Database
Obsolete
Serves as a database collecting matching mRNA sequence amino acid sequence and protein three-dimensional structure data. ISSD generates a total non-redundant set of global pairwise via the measure of actual sequence identity levels. This repository includes a hundred of non-homologous mammalian proteins and be employed to analyse synonymous codon usage patterns in mRNA sequences with correlation with the 3D structure features in the encoded proteins.
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