Paramjeet S. Bagga, Ph.D. |
PROTEINS
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| Atlas
of Protein Side-Chain Interactions
This atlas depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins. |
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| BMRB:
BioMagResBank
A repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids. |
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| CATH
A database that is a hierarchical domain classification of protein structures in the Brookhaven protein databank. Only crystal structures solved to resolution better than 3.0 angstroms are considered, together with NMR structures. |
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| CBS_CPHmodels
A collection of methods and databases developed to predict protein structures. It currently consists of the following tools: CPHmodels: predicts protein structure using comparative (homology) modeling, distanceP: a neural network based method to predict contacts between C-alpha atoms from the amino acid sequence, RedHom: a tool to find a subset with low sequence similarity in a database. |
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| CCDC:
Cambridge Crystallographic Data Centre
The CCDC serves the scientific community through the acquisition, evaluation, dissemination and use of the world's output of small molecule crystal structures by compiling the Cambridge Structural Database, developing scientific products and services, maximizing world-wide accessibility, performing and supporting fundamental research, promoting and supporting applications in academia and industry. |
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| ExPASy_3Dcrunch
The aim of 3Dcrunch is to submit all entries of the SWISS-PROT and trEMBL databases to SWISS-MODEL. Furthermore, all sequences of bacterial origin will be submitted to fold the recognition algorithm implemented in FoldFit. Taken together, these approaches will yield structural models for all sequences with clear similarities to proteins of know 3-D structure and a suggested fold class for all bacterial sequences. |
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| ExPASy_SWISS-MODEL
An automated protein modeling server. The purpose of this server is to make Protein Modeling accessible to all biochemists and molecular biologists World Wide. |
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| HAD:
Heavy Atom Databank
This databank contains: experimental conditions for crystallization, chemical details of the heavy-atom compounds used, atomic coordinates of heavy-atoms, details of binding sites of heavy-atoms/ protein crystal environment, and atomic coordinates of heavy-atoms/ protein crystal environment. |
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| HIV
Protease Database
An archive of experimentally determined 3D structures of HIV-1, HIV-2, and SIV proteases and their complexes. |
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| HSSP:
Homology derived Secondary Structure of Proteins
A database of homology-derived secondary structure of proteins (HSSP) that aligns to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicitly. |
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| ModBase:
Database of Comparative Protein Structure Models
A queryable database of annotated protein structure models. The models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database also includes fold assignments and alignments on which the models were based. MODBASE contains theoretically calculated models, which may contain significant errors, not experimentally determined structures. |
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| NCBI-Structure Group:
The NCBI Structure Group maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. |
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| NCBI_MMDB:
Molecular Modeling DataBase
MMDB contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from PDB. |
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| NCBI-VAST:
Vector Alignment Search Tool
Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the domains in MMDB is compared to every other one. |
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| PDB:
Protein Data Bank
The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR. |
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| Pfam:
Protein Families Database of Alignments and HMMs
A large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam is a collection of protein families and domains. Pfam also contains multiple protein alignments and profile-HMMs of these families. |
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| Protein
Loop Classification
This databank contains conformational clusters and consensus sequences for protein loops that have been derived by computational analysis of their structures in a non-redundant set of proteins with less than 25% sequence homology (X-ray resolution better than 2.5 A). |
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| Protein
Topology
This web site is devoted to protein structural topology and protein topology cartoons. |
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| SBASE
A protein domain library sequences that contains annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to all major sequence databases and sequence pattern collections. |
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| SCOP:
Structural Classification of Proteins
A database that aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in PDB. |
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| TargetDB: Target Search for Structural Genomics
A target registration database funded by the NIH that was originally developed to provide registration and tracking information for the NIH P50 structural genomics centers. A number of other worldwide structural genomics and proteomics projects have also contributed data to TargetDB on a voluntary basis. The scope of TargetDB is to provide timely status and tracking information on the progress of the production and solution of structures. |
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The Molecular Biology Database Collection of NAR (Nucleic Acids Research) |
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