Dataset Information

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

ABSTRACT: STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/.

SUBMITTER: Heinig M

PROVIDER: S-EPMC441567 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

Heinig Matthias M Frishman Dmitrij D

Nucleic acids research 20040701 Web Server issue

STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachan ...[more]

PMID: 15215436

Similar Datasets

Project description:MotivationThe structure of proteins is organized in a hierarchy among which the secondary structure elements, α-helix, β-strand and loop, are the basic bricks. The determination of secondary structure elements usually requires the knowledge of the whole structure. Nevertheless, in numerous experimental circumstances, the protein structure is partially known. The detection of secondary structures from these partial structures is hampered by the lack of information about connecting residues along the primary sequence.ResultsWe introduce a new methodology to estimate the secondary structure elements from the values of local distances and angles between the protein atoms. Our method uses a message passing neural network, named Sequoia, which allows the automatic prediction of secondary structure elements from the values of local distances and angles between the protein atoms. This neural network takes as input the topology of the given protein graph, where the vertices are protein residues, and the edges are weighted by values of distances and pseudo-dihedral angles generalizing the backbone angles ϕ and ψ. Any pair of residues, independently of its covalent bonds along the primary sequence of the protein, is tagged with this distance and angle information. Sequoia permits the automatic detection of the secondary structure elements, with an F1-score larger than 80% for most of the cases, when α helices and β strands are predicted. In contrast to the approaches classically used in structural biology, such as DSSP, Sequoia is able to capture the variations of geometry at the interface of adjacent secondary structure element. Due to its general modeling frame, Sequoia is able to handle graphs containing only Cα atoms, which is particularly useful on low resolution structural input and in the frame of electron microscopy development.Availability and implementationSequoia source code can be found at https://github.com/Khalife/Sequoia with additional documentation.Supplementary informationSupplementary data are available at Bioinformatics Advances online.

Dataset Information

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

Publications

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets