scholarly journals Protein Structure Annotation Resources

2014 ◽  
pp. 3-20 ◽  
Author(s):  
Margaret J. Gabanyi ◽  
Helen M. Berman
Keyword(s):  
Protein Structure ◽  
Structure Annotation

scholarly journals Accurate Protein Structure Annotation through Competitive Diffusion of Enzymatic Functions over a Network of Local Evolutionary Similarities

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e14286 ◽  
Author(s):  
Eric Venner ◽  
Andreas Martin Lisewski ◽  
Serkan Erdin ◽  
R. Matthew Ward ◽  
Shivas R. Amin ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure Annotation ◽  
Competitive Diffusion

scholarly journals ProSAT2--Protein Structure Annotation Server

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W79-W83 ◽  
Author(s):  
R. R. Gabdoulline ◽  
S. Ulbrich ◽  
S. Richter ◽  
R. C. Wade
Keyword(s):  
Protein Structure ◽  
Annotation Server ◽  
Structure Annotation

scholarly journals Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation

2019 ◽  
Vol 48 (D1) ◽  
pp. D314-D319 ◽  
Author(s):  
Ian Sillitoe ◽  
Antonina Andreeva ◽  
Tom L Blundell ◽  
Daniel W A Buchan ◽  
Robert D Finn ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Protein Structure ◽  
Scientific Community ◽  
Protein Sequences ◽  
Model Organisms ◽  
Annotation Data ◽  
Data Pipeline ◽  
Structure Annotation ◽  
Representative Protein ◽  
Selection Of

Abstract Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being ‘pushed’ to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.

Sequence Specific Dihedral Angle Distribution: Application in Protein Structure Prediction and Evaluation

1970 ◽  
Vol 19 (2) ◽  
pp. 217-226
Author(s):  
S. M. Minhaz Ud-Dean ◽  
Mahdi Muhammad Moosa
Keyword(s):  
Protein Structure ◽  
Dihedral Angle ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Protein Structures ◽  
Angle Distribution ◽  
Ramachandran Plot ◽  
Specific Data ◽  
Specific Distribution ◽  
Structure Evaluation

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)

Protein structure prediction of human connexin 30 and its mutations in hearing system

2014 ◽  
Vol 3 (5) ◽  
Author(s):  
S. Reiisi ◽  
M. Hashemzade-chaleshtori ◽  
S. Reisi ◽  
H. Shahi ◽  
S. Parchami ◽  
...  
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Connexin 30 ◽  
Hearing System
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