3D structure of proteins
From MyBio
This article contains resourcse on the tertiary or 3D structure of proteins.
Contents |
[edit] Categories which link here
[edit] Related subcategories
- 3D Structure Tools
- Imaging Tools
- Databases of protein tertiary structures
- Protein structure visualization
- 3D protein structure tutorials
- 3D structure alignment
- Threading
- Solvent accessibility
- 3D structure search
- 3D structure evaluation
- Disulfide bonding state prediction
[edit] 3D structure of proteins - Quick Links
| Geno3D | Visual Molecular Dynamics | |
| PINTS | TOPS | |
| (PS)2: Protein Structure Prediction Server | DiANNA: unified software for Cysteine state and Disulfide Bond partner prediction | |
| Jean-Christophe Nebel |
[edit] 3D structure of proteins - Web Resources
| DPL Forum: Too few categories! |
MMDB (Molecular Modeling Database) annotating protein sequences with Entrez's 3D-structure database. 3D structure is known for a large fraction of all protein families (2006). Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers.
Entrez's ‘Related Structure’ links provide easy access to the richness of 3D structure data and its large potential for functional annotation, presenting 3D views mapping sequence residues onto all 3D structures available in MMDB. 
Geno3D
Automatic modeling of protein 3D structure.
Visual Molecular Dynamics
NIH Resource for Macromolecular Modeling and Bioinformatics.
PINTS
Patterns in Non-homologous Tertiary Structures - Annotation in three dimensions. The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures performs database searches for such patterns and most importantly provides a measure of statistical significance for any similarity uncovered. To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important.
TOPS
An enhanced database of protein structural topology. The TOPS database holds topological descriptions of protein structures. These compact and highly abstract descriptions reduce the protein fold to a sequence of Secondary Structure Elements (SSEs) and three sets of pairwise relationships between them, hydrogen bonds relating parallel and anti-parallel beta strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in beta-alpha-beta units and between parallel alpha helices. The database is used as a resource for visualizing folding topologies, fast topological pattern searching and structure comparison.
(PS)2: Protein Structure Prediction Server
Automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment. The final three dimensional structure is built using MODELLER.
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DiANNA: unified software for Cysteine state and Disulfide Bond partner prediction
Predicts cysteine oxidation states of proteins. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand. Outputs the disulfide connectivity prediction given input of a protein sequence.
| Image:Protein.jpg |
| Jean-Christophe Nebel |
