Advertisement

Topics

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

08:00 EDT 21st May 2018 | BioPortfolio

Summary of "mTM-align: a server for fast protein structure database search and multiple protein structure alignment."

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Affiliation

Journal Details

This article was published in the following journal.

Name: Nucleic acids research
ISSN: 1362-4962
Pages:

Links

DeepDyve research library

PubMed Articles [26819 Associated PubMed Articles listed on BioPortfolio]

MDockPeP: An ab-initio protein-peptide docking server.

Protein-peptide interactions play a crucial role in a variety of cellular processes. The protein-peptide complex structure is a key to understand the mechanisms underlying protein-peptide interactions...

Identification and visualization of protein binding regions with the ArDock server.

ArDock (ardock.ibcp.fr) is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. ArDock ranks the surface residues of a ...

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poor...

CDB-a database for protein heterodimeric complexes.

Crystallographic structures of protein complexes are essential to develop proteomic and structural biology methods, as prediction of protein-protein interaction (PPI) sites and protein-protein docking...

Translocatome: a novel resource for the analysis of protein translocation between cellular organelles.

Here we present Translocatome, the first dedicated database of human translocating proteins (URL: http://translocatome.linkgroup.hu). The core of the Translocatome database is the manually curated dat...

Clinical Trials [8075 Associated Clinical Trials listed on BioPortfolio]

Clinical and Laboratory Online Patient- and Research Database for Primary Immunodeficiencies in Switzerland

A Swiss national, multi-centre, online patient and research database will be created, using the existing ESID database server system. This database contains disease-specific data from pati...

PRO-STATE:Search for a Protein Profile Corresponding to Fast-Developing Lesions and Characterization of Implicated Proteins in Prostate Carcinoma

The main objective of this study is to realise serum protein profiles for each patient undergoing a prostate biopsy and to identify relevant proteins.

International AGD Database; Determinants of AGD and Establishment of Normative Data

Aim: To collate data on Anogenital Distance (AGD) from several population studies to build an international database for Anogenital Distance (AGD) Primary objective: To build a database p...

Open Access Database of Standing Full Body Radiographs in Asymptomatic Volunteers

A study of the skeletal structure and how the structure changes over time. The aim of the study is to evaluate the skeleton in 10 year increments to determine an understanding of the norma...

Bergonie Institute Breast Cancer Database

A database of breast cancer patients was established at Institute Bergonié since the 90s , to assess patients' survival, assess practice, search for prognostic factors.

Medical and Biotech [MESH] Definitions

The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.

Devices used to support or align the foot structure, or to prevent or correct foot deformities.

The three-part structure of ribbon-like proteinaceous material that serves to align and join the paired homologous CHROMOSOMES. It is formed during the ZYGOTENE STAGE of the first meiotic division. It is a prerequisite for CROSSING OVER.

A group I chaperonin protein that forms the barrel-like structure of the chaperonin complex. It is an oligomeric protein with a distinctive structure of fourteen subunits, arranged in two rings of seven subunits each. The protein was originally studied in BACTERIA where it is commonly referred to as GroEL protein.

The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Relevant Topic

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...


Searches Linking to this Article