scholarly journals Resdiue-residue contact driven protein structure prediction using optimization and machine learning

2017 ◽  
Author(s):  
◽  
Badri Adhikari
Keyword(s):  
Machine Learning ◽  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structures ◽  
Contact Prediction ◽  
Residue Contacts ◽  
Structure Reconstruction ◽  
Ab Initio Structure

Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps, tools to assess the utility of predicted contacts, and methods to construct protein tertiary structures from predicted contacts, are essential to further improve ab initio structure prediction. In this dissertation, three contributions are described -- (a) DNCON2, a two-level convolutional neural network-based method for protein contact prediction, (b) ConEVA, a toolkit for contact assessment and evaluation, and (c) CONFOLD, a method of building protein 3D structures from predicted contacts and secondary structures. Additional related contributions on protein contact prediction and structure reconstruction are also described. DNCON2 and CONFOLD demonstrate state-of-the-art performance on contact prediction and structure reconstruction from scratch. All three protein structure methods are available as software or web server which are freely available to the scientific community.

scholarly journals FALCON2: a web server for high-quality prediction of protein tertiary structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lupeng Kong ◽  
Fusong Ju ◽  
Haicang Zhang ◽  
Shiwei Sun ◽  
Dongbo Bu
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Web Server ◽  
High Quality ◽  
Tertiary Structures ◽  
Target Proteins ◽  
High Quality Protein ◽  
Protein Functions

Abstract Background Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a template-based modeling approach (called ProALIGN) and an ab initio prediction approach (called ProFOLD). Briefly speaking, ProALIGN aligns a target protein with templates through exploiting the patterns of context-specific alignment motifs and then builds the final structure with reference to the homologous templates. In contrast, ProFOLD uses an end-to-end neural network to estimate inter-residue distances of target proteins and builds structures that satisfy these distance constraints. These two approaches emphasize different characteristics of target proteins: ProALIGN exploits structure information of homologous templates of target proteins while ProFOLD exploits the co-evolutionary information carried by homologous protein sequences. Recent progress has shown that the combination of template-based modeling and ab initio approaches is promising. Results In the study, we present FALCON2, a web server that integrates ProALIGN and ProFOLD to provide high-quality protein structure prediction service. For a target protein, FALCON2 executes ProALIGN and ProFOLD simultaneously to predict possible structures and selects the most likely one as the final prediction result. We evaluated FALCON2 on widely-used benchmarks, including 104 CASP13 (the 13th Critical Assessment of protein Structure Prediction) targets and 91 CASP14 targets. In-depth examination suggests that when high-quality templates are available, ProALIGN is superior to ProFOLD and in other cases, ProFOLD shows better performance. By integrating these two approaches with different emphasis, FALCON2 server outperforms the two individual approaches and also achieves state-of-the-art performance compared with existing approaches. Conclusions By integrating template-based modeling and ab initio approaches, FALCON2 provides an easy-to-use and high-quality protein structure prediction service for the community and we expect it to enable insights into a deep understanding of protein functions.

scholarly journals Ab Initio Protein Structure Prediction Using Pathway Models

2003 ◽  
Vol 4 (4) ◽  
pp. 397-401 ◽  
Author(s):  
Xin Yuan ◽  
Yu Shao ◽  
Christopher Bystroff
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Pathway Models

AIMOES: Archive information assisted multi-objective evolutionary strategy for ab initio protein structure prediction

2018 ◽  
Vol 146 ◽  
pp. 58-72 ◽  
Author(s):  
Shuangbao Song ◽  
Shangce Gao ◽  
Xingqian Chen ◽  
Dongbao Jia ◽  
Xiaoxiao Qian ◽  
...  
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Evolutionary Strategy ◽  
Multi Objective

Protein Structure Prediction

Biotechnology ◽  
2019 ◽  
pp. 156-184
Author(s):  
Hirak Jyoti Chakraborty ◽  
Aditi Gangopadhyay ◽  
Sayak Ganguli ◽  
Abhijit Datta
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Future Research ◽  
Computational Techniques ◽  
Target Sequence ◽  
Knowledge Based ◽  
Research Areas ◽  
Three Phases

The great disagreement between the number of known protein sequences and the number of experimentally determined protein structures indicate an enormous necessity of rapid and accurate protein structure prediction methods. Computational techniques such as comparative modeling, threading and ab initio modelling allow swift protein structure prediction with sufficient accuracy. The three phases of computational protein structure prediction comprise: the pre-modelling analysis phase, model construction and post-modelling refinement. Protein modelling is primarily comparative or ab initio. Comparative or template-based methods such as homology and threading-based modelling require structural templates for constructing the structure of a target sequence. The ab initio is a template-free modelling approach which proceeds by satisfying various physics-based and knowledge-based parameters. The chapter will elaborate on the three phases of modelling, the programs available for performing each, issues, possible solutions and future research areas.

Protein Structure Prediction

2018 ◽  
pp. 48-79 ◽  
Author(s):  
Hirak Jyoti Chakraborty ◽  
Aditi Gangopadhyay ◽  
Sayak Ganguli ◽  
Abhijit Datta
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Future Research ◽  
Computational Techniques ◽  
Target Sequence ◽  
Knowledge Based ◽  
Research Areas ◽  
Three Phases

The great disagreement between the number of known protein sequences and the number of experimentally determined protein structures indicate an enormous necessity of rapid and accurate protein structure prediction methods. Computational techniques such as comparative modeling, threading and ab initio modelling allow swift protein structure prediction with sufficient accuracy. The three phases of computational protein structure prediction comprise: the pre-modelling analysis phase, model construction and post-modelling refinement. Protein modelling is primarily comparative or ab initio. Comparative or template-based methods such as homology and threading-based modelling require structural templates for constructing the structure of a target sequence. The ab initio is a template-free modelling approach which proceeds by satisfying various physics-based and knowledge-based parameters. The chapter will elaborate on the three phases of modelling, the programs available for performing each, issues, possible solutions and future research areas.

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