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Tools for comparative protein structure modeling and analysis

N. Eswar
2003 Nucleic Acids Research  
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB  ...  of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure  ...  SOFTWARE AND WEB SERVERS MODELLER MODELLER is a computer program for comparative protein structure modeling (http://salilab.org/modeller) (17, 18) .  ... 
doi:10.1093/nar/gkg543 pmid:12824331 pmcid:PMC168950 fatcat:7h4x7vmc7rbh7nzath35dod2x4

Homology Modeling, Functional Annotation and Comparative Genome Analysis of GBSS Enzyme in Rice and Maize Genomes
English

Javed Iqbal Wattoo, Muhammad Shahzad Iqbal, Muhammad Arif, Zafar Saleem, Muhammad Naveed Shahid, Muhammad Iqbal
2015 International Journal of Agriculture and Biology  
Shahid and M. Iqbal, 2015. Homology modeling, functional annotation and comparative genome analysis of GBSS enzyme in rice and maize genomes.  ...  We have interpreted homology modeling, functional annotation and comparative genome analysis of waxy gene among rice and maize genomes.  ...  The authors wish to thank the anonymous reviewers for their valuable suggestions and thoughtful comments.  ... 
doi:10.17957/ijab/15.0016 fatcat:ixmcswuknnht5h5iea2le4b4ca

DINAMO: interactive protein alignment and model building

J Bentz, A Baucom, M Hansen, L Gregoret
1999 Bioinformatics  
Motivation: To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool  ...  DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein structure by means of a set of analysis tools.  ...  Acknowledgements We would like to thank Leslie Grate for providing the inspiration for DINAMO and for allowing us to use his inhouse prototype program, SAE.  ... 
doi:10.1093/bioinformatics/15.4.309 pmid:10320399 fatcat:ojeeiiovazfl5kiws3nxfhe7na

Comparative modeling, structure and active site prediction of Sclerotinia disease-resistant gene BnaMPK3 in Oilseed rape (Brassica napus)

Haider Zeshan, Zulfiqar Muzdalfa, Rana Iqrar Ahmad, Ahmad Khan Rao Sohail, Akram Muhammad Numan, Niazi Adnan Khan
2020 Open Journal of Bioinformatics and Biostatistics  
This could be possible through in Insilco analysis of protein through protein comparative modeling which is a recent and important technique, used for the prediction of the protein three-dimensional (3D  ...  The comparative modeling of the BnaMPK3 protein through Swiss-Model predicted 76.88% identity with template 6dtl.2A. 3-D structure of BnaMPK3 protein was validated through Errat score, which was 93.023%  ...  It is an online web computational tool used for the homology modeling of protein three-dimensional structure [16] .  ... 
doi:10.17352/ojbb.000005 fatcat:kdgytkvffvdpjb4symslf3uetq

Prediction of a highly deleterious mutation E17K in AKT-1 gene: An in silico approach

Imran Khan, Irfan A. Ansari
2017 Biochemistry and Biophysics Reports  
The insight of the structural attribute was gained through analysis of, secondary structures, solvent accessibility and intermolecular hydrogen bond analysis which confirmed one missense mutation (E17K  ...  RMSD values were calculated for the mutant models which predicted four substitutions (E17K, E319G, D32E and A255T) to be highly deleterious.  ...  Acknowledgments The authors thank the management of the Integral University for providing the facilities to carry out this study.  ... 
doi:10.1016/j.bbrep.2017.04.013 pmid:29114575 pmcid:PMC5637233 fatcat:m4tamsguj5bltkmnxtor3h4nh4

Sequence and structural Analysis of β- actin Protein of fishes, using Bioinformatics Tools and techniques

2014 International Journal of Biosciences  
In the present study, a bioinformatics approach has been adopted to explore the sequence, structure and phylogenetic analysis of β-actin protein from eight commercially important fishes and compared with  ...  For establishing evolutionary inter-relationship, sequence analysis and alignment of protein sequences, seems to be crucial.  ...  Acknowledgements The authors thankfully acknowledge DBT, Govt. of India for financial assistance and to the Head, P.G.Dept. of Zoology for providing necessary laboratory facilities.  ... 
doi:10.12692/ijb/4.11.249-256 fatcat:yp262nal7jhlnogxec72dnic2e

The Path to Enlightenment: Making Sense of Genomic and Proteomic Information

Martin H. Maurer
2004 Genomics, Proteomics & Bioinformatics  
Tools for comparative modeling of protein structures include COMPOSER, DRAGON, WhatIf, a versatile protein structure analysis program that can be used for mutant prediction, structure verification, and  ...  It provides several tools for protein structure analysis, such as modeling algorithms. All information is presented in units and is useful for self-study.  ...  Other publications collected bioinformatic tools available at the Internet and may be consulted for additional resources (44) (45) (46) .  ... 
doi:10.1016/s1672-0229(04)02018-2 pmid:15629052 pmcid:PMC5172447 fatcat:ijlzaqhr7rdihbhhv6srpsydfi

In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene

Sayed AbdulAzeez, J. Francis Borgio, Yang Zhang
2016 PLoS ONE  
Conclusions A total of 5 nsSNPs (G60V, K17M, K17T, L92F and W15R) were predicted to be responsible for the structural and functional modifications of HBA1 protein.  ...  These "2 pathogenic nsSNPs" can be considered for wet-lab confirmatory analysis.  ...  Structure Modeling and Stability Check The 3D structure for HBA1 protein was modeled based on a template PDB id-1y01.1.B (From ExPDB) to compare and understand the significant effect of mutations, in the  ... 
doi:10.1371/journal.pone.0147702 pmid:26824843 pmcid:PMC4733110 fatcat:nejidv4hanai5j3cm4nvqm6nfa

Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237

Azeem Mehmood Butt, Maria Batool, Yigang Tong
2011 Bioinformation  
Among these, 94 are without any known function and are described as 'hypothetical proteins'. We selected MG_237 for sequence and structural analysis using a bioinformatics approach.  ...  Furthermore, comparative genomics analysis suggested MG_237 as non-homologous protein and involved in four different metabolic pathways.  ...  Imran Mehmood Butt for his assistance in preparing graphical illustrations.  ... 
doi:10.6026/007/97320630007299 pmid:22355225 pmcid:PMC3280499 fatcat:tqgzwmfxvjdyrae23z6qk5nqme

Cross-Species Amino Acids Sequence Comparison and Computational Docking of Human IL-1Ra and Rat IL-1Ra on Rat Receptor

Muhammad Sajid
2013 Journal of Proteomics & Bioinformatics  
Acknowledgments Authors would like to acknowledge China Scholarship council to provide scholarships to Muhammad Sajid Hamid Akash and Kanwal Rehman for their PhD studies.  ...  This work was partially supported by the grant (No. 2010C13006) from the Science and Technology Department of Zhejiang Province, China.  ...  Discussion Use of computer modeling to predict 3D protein structure is an alternate tool for the investigation of structural and functional relationship of desired protein in cross-species.  ... 
doi:10.4172/jpb.1000259 fatcat:glntt3sa6zezfo4q3pdf2dxc5m

Structure modeling to function prediction of Uncharacterized Human Protein C15orf41

Md. Shakil Ahmed, Md. Shahjaman, Enamul Kabir, Md. Kamruzzaman
2018 Bioinformation  
The uncharacterized C15orf41 protein is involved in the formation of a functional complex structure. The uncharacterized C15orf41 protein is thermostable, unstable and acidic.  ...  It interacts with the human ATP (Adenosine Triphosphate) binding domain 4 (ATPBD4) having similarity score 0.725 as per protein-protein interaction (PPI) network analysis.  ...  These tools are widely used for homology modeling of sequence profiles and predicting the three-dimensional (3D) structure of the targeted protein.  ... 
doi:10.6026/97320630014206 pmid:30108417 pmcid:PMC6077826 fatcat:piwqj7bv6fhs7cb3xp4hkrl2su

Comparative Structure Modeling of Glyoxalase II Protein of Oryza sativa

Ramandeep Kaur Jhinjer, Naveen Duhan, Parveen Chhuneja
2017 International Journal of Current Microbiology and Applied Sciences  
This model can be used for further analysis for different studies. both the cytosol and mitochondria.  ...  Comparative Structure Modeling Tertiary structure of the "target" protein from its amino acid sequence is build by homology modeling by using four online tools (SWISS-MODEL, CPH models 3.0 Server, I-TASSER  ... 
doi:10.20546/ijcmas.2017.608.168 fatcat:xcnxsu4gqjbldf43c3fdnaeolq

The MPI Bioinformatics Toolkit for protein sequence analysis

A. Biegert, C. Mayer, M. Remmert, J. Soding, A. N. Lupas
2006 Nucleic Acids Research  
One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool.  ...  Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view.  ...  ACKNOWLEDGEMENTS We thank Pawel Szczesny for contributing Aln2Plot and Tancrd Frickey for many fruitful discussions and developing various tools.  ... 
doi:10.1093/nar/gkl217 pmid:16845021 pmcid:PMC1538786 fatcat:o7tpiafv7rgzvnehf4o4zmjgxe

IN SILICO PREDICTION OF DELETERIOUS AND NON-DELETERIOUS nsSNPs IN CFTR GENE VARIANTS

Vemulapati Bhadra Murthy, Meghana Chowdary, Sucharitha .
2016 International Journal of Pharmacy and Pharmaceutical Sciences  
(b) PolyPhen2: a structure and sequence-based physical and comparison tool to study the impact of amino acid substitution on the structure and function of human proteins and (c) I-Mutant2: to predict the  ...  structure and functions of CFTR protein causing cystic fibrosis.  ...  Homology (or comparative) modeling methods make use of experimental protein structures ("templates") to build models for evolutionarily related proteins ("targets").  ... 
doi:10.22159/ijpps.2016v8i12.14737 fatcat:zwq2yxfnc5diroizqxzqxb5qpe

Integration of Bioinformatics Tools for Proteomics Research

Tushar Nanda, Kadambini Tripathy
2011 Journal of computer science and systems biology  
An emerging field for the analysis of biological systems is the study of the complete protein complement of the genome, the 'proteome'.  ...  Emerging proteomic technologies have promised for early diagnosis and in advancing treatment directions.  ...  Comparative Modeling Of Viral Protein R (Vpr) From Human Immunodeficiency Virus 1 (Hiv 1) is done to predict the structure of a VpR using NMR structure of the HIV-1 regulatory protein as the template (  ... 
doi:10.4172/jcsb.s13-002 fatcat:k3d5kuw3vbcxzi5a3dopmmnlwq
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