scholarly journals Efficient Screening for Ternary Molecular Ionic Cocrystals Using a Complementary Mechanosynthesis and Computational Structure Prediction Approach

2020 ◽  
Vol 26 (21) ◽  
pp. 4752-4765 ◽  
Author(s):  
Abeer F. Shunnar ◽  
Bhausaheb Dhokale ◽  
Durga Prasad Karothu ◽  
David H. Bowskill ◽  
Isaac J. Sugden ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Computational Structure ◽  
Prediction Approach ◽  
Efficient Screening

Computational structure determination of novel metal–organic frameworks

2018 ◽  
Vol 54 (77) ◽  
pp. 10812-10815 ◽  
Author(s):  
Mohammad Wahiduzzaman ◽  
Sujing Wang ◽  
Benjamin J. Sikora ◽  
Christian Serre ◽  
Guillaume Maurin
Keyword(s):  
Structure Determination ◽  
Structure Prediction ◽  
Metal Organic Frameworks ◽  
Prediction Tool ◽  
Computational Structure ◽  
Metal Organic

A structure prediction tool has been developed to guide the discovery of MOF materials.

Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken

2019 ◽  
Vol 126 ◽  
pp. 139-149
Author(s):  
P. Guru Vishnu ◽  
T.K. Bhattacharya ◽  
Bharat Bhushan ◽  
Pushpendra Kumar ◽  
R.N. Chatterjee ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Structure Prediction ◽  
Broiler Chicken ◽  
Receptor Type ◽  
Activin Receptor ◽  
Computational Structure

scholarly journals Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on

2020 ◽  
Vol 15 (6) ◽  
pp. 611-628
Author(s):  
Jad Abbass ◽  
Jean-Christophe Nebel
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Protein Design ◽  
Structure Prediction ◽  
De Novo ◽  
Protein Docking ◽  
Ligand Docking ◽  
Ancient Egyptian ◽  
Docking Protein ◽  
Prediction Approach

For two decades, Rosetta has consistently been at the forefront of protein structure prediction. While it has become a very large package comprising programs, scripts, and tools, for different types of macromolecular modelling such as ligand docking, protein-protein docking, protein design, and loop modelling, it started as the implementation of an algorithm for ab initio protein structure prediction. The term ’Rosetta’ appeared for the first time twenty years ago in the literature to describe that algorithm and its contribution to the third edition of the community wide Critical Assessment of techniques for protein Structure Prediction (CASP3). Similar to the Rosetta stone that allowed deciphering the ancient Egyptian civilisation, David Baker and his co-workers have been contributing to deciphering ’the second half of the genetic code’. Although the focus of Baker’s team has expended to de novo protein design in the past few years, Rosetta’s ‘fame’ is associated with its fragment-assembly protein structure prediction approach. Following a presentation of the main concepts underpinning its foundation, especially sequence-structure correlation and usage of fragments, we review the main stages of its developments and highlight the milestones it has achieved in terms of protein structure prediction, particularly in CASP.

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.

HPS_PSP: HIGH PERFORMANCE SYSTEM FOR PROTEIN STRUCTURE PREDICTION

2019 ◽  
Vol 27 (04) ◽  
pp. 487-502
Author(s):  
MOHAMED B. ABDELHALIM ◽  
MAI S. MABROUK ◽  
AHMED Y. SAYED
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
High Performance ◽  
Neighborhood Search ◽  
Efficient Design ◽  
Local Optima ◽  
Genetic Operator ◽  
Comparative Results ◽  
Prediction Approach

Prediction of least energy conformation of a protein from its primary structure (chain of amino acids) is an optimization problem associated with a large complex energy landscape. In this study, a simple 2D hydrophobic–hydrophilic model was used to model the protein sequence, which allows the fast and efficient design of genetic algorithm-based protein structure prediction approach. The neighborhood search strategy is integrated into the genetic operator. The neighborhood search guides the genetic operator to regions in the computational space with good solutions. To prevent convergence to local optima, the proposed method employs crowding-based parent replacement strategy, which improves the performance of the algorithm and the ability to deal with multiple numbers of solutions. The proposed algorithm was tested with a standard benchmark of HP sequences and comparative results demonstrate that the proposed system beats most of the evolutionary algorithms for seven sequences. It finds the best energy for a sequence of length [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text].

scholarly journals Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e23947 ◽  
Author(s):  
Christopher S. Poultney ◽  
Glenn L. Butterfoss ◽  
Michelle R. Gutwein ◽  
Kevin Drew ◽  
David Gresham ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Rational Design ◽  
Temperature Sensitive ◽  
Computational Structure
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