scholarly journals Three-dimensional (3D) structure prediction and function analysis of the chitin-binding domain 3 protein HD73_3189 from Bacillus thuringiensis HD73

2015 ◽  
Vol 26 (s1) ◽  
pp. S2019-S2024 ◽  
Author(s):  
Yiling Zhan ◽  
Shuyuan Guo
Keyword(s):  
Bacillus Thuringiensis ◽  
Structure Prediction ◽  
Function Analysis ◽  
3D Structure ◽  
Three Dimensional ◽  
Binding Domain ◽  
Chitin Binding Domain ◽  
3D Structure Prediction ◽  
Domain 3 ◽  
And Function

Molecular cloning and 3D structure prediction of the first raw-starch-degrading glucoamylase without a separate starch-binding domain

2003 ◽  
Vol 411 (2) ◽  
pp. 189-195 ◽  
Author(s):  
Eva Hostinová ◽  
Adriana Solovicová ◽  
Radovan Dvorský ◽  
Juraj Gašperı́k
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Binding Domain ◽  
Raw Starch ◽  
3D Structure Prediction

scholarly journals Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

2014 ◽  
Vol 10 (3) ◽  
pp. 130-137 ◽  
Author(s):  
Edina Wang ◽  
◽  
Suresh Chinni ◽  
Subhash Janardhan Bhore
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Comparative Modelling ◽  
Oil Palms ◽  
3D Structure Prediction

scholarly journals Using AlphaFold to predict the impact of single mutations on protein stability and function

2021 ◽  
Author(s):  
Marina A Pak ◽  
Karina A Markhieva ◽  
Mariia S Novikova ◽  
Dmitry S Petrov ◽  
Ilya S Vorobyev ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Structure Prediction ◽  
Large Scale ◽  
3D Structure ◽  
Three Dimensional ◽  
Single Mutation ◽  
Before And After ◽  
And Function ◽  
The Impact

AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is "solved". However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the AlphaFold predictions on the impact of a single mutation on structure with a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold cannot be immediately applied to other problems or applications in protein folding.

scholarly journals Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis

2013 ◽  
Vol 9 (14) ◽  
pp. 725-729 ◽  
Author(s):  
Ujala Sehar ◽  
◽  
Muhammad Aamer Mehmood ◽  
Salman Nawaz ◽  
Shahid Nadeem ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Structure Prediction ◽  
Binding Protein ◽  
3D Structure ◽  
Three Dimensional ◽  
Interaction Study ◽  
Substrate Protein ◽  
3D Structure Prediction ◽  
Chitin Binding Protein

In silico 3D structure prediction and hydrogen peroxide binding study of wheat catalase

2013 ◽  
Vol 5 (1) ◽  
pp. 77-83 ◽  
Author(s):  
Gopal Krishna Sahu ◽  
Bibhuti Bhusan Sahoo ◽  
Sneha Bhandari ◽  
Shruti Pandey
Keyword(s):  
Hydrogen Peroxide ◽  
In Silico ◽  
Structure Prediction ◽  
3D Structure ◽  
Binding Study ◽  
3D Structure Prediction

scholarly journals Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 432 ◽  
Author(s):  
Chandran Nithin ◽  
Pritha Ghosh ◽  
Janusz Bujnicki
Keyword(s):  
Rna Splicing ◽  
Structure Prediction ◽  
Protein Complexes ◽  
3D Structure ◽  
Structural Models ◽  
Computational Prediction ◽  
Computational Docking ◽  
3D Structure Prediction ◽  
Rna Protein Complexes

RNA-protein (RNP) interactions play essential roles in many biological processes, such as regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing, transport, storage and stabilization, as well as protein synthesis. An increasing number of RNP structures would aid in a better understanding of these processes. However, due to the technical difficulties associated with experimental determination of macromolecular structures by high-resolution methods, studies on RNP recognition and complex formation present significant challenges. As an alternative, computational prediction of RNP interactions can be carried out. Structural models obtained by theoretical predictive methods are, in general, less reliable compared to models based on experimental measurements but they can be sufficiently accurate to be used as a basis for to formulating functional hypotheses. In this article, we present an overview of computational methods for 3D structure prediction of RNP complexes. We discuss currently available methods for macromolecular docking and for scoring 3D structural models of RNP complexes in particular. Additionally, we also review benchmarks that have been developed to assess the accuracy of these methods.

scholarly journals Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk

Sequencing ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Amitava Moulick ◽  
Debashis Mukhopadhyay ◽  
Shonima Talapatra ◽  
Nirmalya Ghoshal ◽  
Sarmistha Sen Raychaudhuri
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Transcript Level ◽  
Copper Stress ◽  
Dimensional Structure ◽  
Functional Study ◽  
Plantago Ovata

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

scholarly journals 1P241 An exhaustive modeling and evaluation system in protein 3D structure prediction pipeline FORTE-SUITE(Bioinformatics-structural genomics,Poster Presentations)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S83
Author(s):  
Chie Motono ◽  
Takatsugu Hirokawa ◽  
Miwa Sato ◽  
Yasuhiro Fujihara ◽  
Kiyotaka Kisoo ◽  
...  
Keyword(s):  
Structural Genomics ◽  
Structure Prediction ◽  
Evaluation System ◽  
3D Structure ◽  
Protein 3D Structure ◽  
3D Structure Prediction ◽  
Poster Presentations

scholarly journals 3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0122223 ◽  
Author(s):  
Zaheer Ul-Haq ◽  
Maria Saeed ◽  
Sobia Ahsan Halim ◽  
Waqasuddin Khan
Keyword(s):  
Homology Modeling ◽  
Adrenergic Receptor ◽  
Structure Prediction ◽  
3D Structure ◽  
Drug Designing ◽  
3D Structure Prediction

Automated RNA 3D Structure Prediction with RNAComposer

2016 ◽  
pp. 199-215 ◽  
Author(s):  
Marcin Biesiada ◽  
Katarzyna J. Purzycka ◽  
Marta Szachniuk ◽  
Jacek Blazewicz ◽  
Ryszard W. Adamiak
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
3D Structure Prediction
Sign in / Sign up

Export Citation Format

Share Document