scholarly journals Selective refinement and selection of near-native models in protein structure prediction

2015 ◽  
Vol 83 (10) ◽  
pp. 1823-1835 ◽  
Author(s):  
Jiong Zhang ◽  
Bogdan Barz ◽  
Jingfen Zhang ◽  
Dong Xu ◽  
Ioan Kosztin
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Selection Of

scholarly journals Basic protein structure prediction for the biologist: A review

2010 ◽  
Vol 62 (4) ◽  
pp. 857-871 ◽  
Author(s):  
M. Mihăşan
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Basic Protein ◽  
Point Of View ◽  
Exponential Rate ◽  
Computational Structure ◽  
Number Of Citations ◽  
Selection Of

As the field of protein structure prediction continues to expand at an exponential rate, the bench-biologist might feel overwhelmed by the sheer range of available applications. This review presents the three main approaches in computational structure prediction from a non-bioinformatician?s point of view and makes a selection of tools and servers freely available. These tools are evaluated from several aspects, such as number of citations, ease of usage and quality of the results. Finally, the applications of models generated by computational structure prediction are discussed.

scholarly journals ROPIUS0: A deep learning-based protocol for protein structure prediction and model selection and its performance in CASP14

2021 ◽  
Author(s):  
Mindaugas Margelevicius
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Model Selection ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Homologous Proteins ◽  
Tertiary Structure Prediction ◽  
Direct Use ◽  
Selection Of

A protocol ROPIUS0 for protein structure prediction and model selection is presented. At the core of the ROPIUS0 protocol is the deep learning module developed for the selection of protein structural models. It is shown that the direct use of predicted inter-residue distances may be sufficient to discriminate between correct and incorrect protein folds, considering only a small fraction of predicted distances. Having finished the latest CASP14 prediction season, a ROPIUS0 variant based on model selection ranks 13th in the category of tertiary structure prediction. Its performance is on par with top-performing automated prediction servers when tested on the CASP13 dataset. The results suggest ways to improve searching for structurally similar and homologous proteins without considerably increasing speed.

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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