Identifying redox-sensitive extra-chloroplastic enzymes by homology modeling

2000 ◽  
Vol 110 (3) ◽  
pp. 296-302
Author(s):  
Louise E. Anderson ◽  
Alex Dong Li ◽  
Elizabeth H. Muslin ◽  
Marianne Schiffer ◽  
Fred J. Stevens
Keyword(s):  
Homology Modeling

Unveiling the Accuracy of Homology Modeling to Elucidate the Structure of GPCRs-HIV Co-receptor-CCR5 as a Case Study

2018 ◽  
Vol 15 (10) ◽  
pp. 1068-1078
Author(s):  
Vadivelu Aanand ◽  
Rajendran Anitha ◽  
Somarathinam Kanagasabai ◽  
Gunalan Seshan ◽  
Changdev G. Gadhe ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Receptor Ccr5

LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

2019 ◽  
Vol 15 (4) ◽  
pp. 353-362
Author(s):  
Sambhaji B. Thakar ◽  
Maruti J. Dhanavade ◽  
Kailas D. Sonawane
Keyword(s):  
Phylogenetic Analysis ◽  
Medicinal Plants ◽  
Homology Modeling ◽  
Sequence Alignment ◽  
Vigna Unguiculata ◽  
Multiple Sequence Alignment ◽  
Legume Species ◽  
Mangrove Species ◽  
Multiple Sequence ◽  
Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

Homology Modeling Inspired Synthesis of 5-HT2A Receptor Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13

2017 ◽  
Vol 17 (3) ◽  
Author(s):  
Enrico Mongeau ◽  
Gengyang Yuan ◽  
Zachary Minden ◽  
Scott Waldron ◽  
Raymond Booth ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Atypical Antipsychotic

scholarly journals PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

2012 ◽  
Vol 13 (Suppl 4) ◽  
pp. S2 ◽  
Author(s):  
Emanuele Bramucci ◽  
Alessandro Paiardini ◽  
Francesco Bossa ◽  
Stefano Pascarella
Keyword(s):  
Homology Modeling ◽  
Sequence Similarity ◽  
Sequence Structure ◽  
Multiple Sequence ◽  
Similarity Searches

scholarly journals Structure-Function Analysis of IntDOT

2009 ◽  
Vol 192 (2) ◽  
pp. 575-586 ◽  
Author(s):  
Seyeun Kim ◽  
Brian M. Swalla ◽  
Jeffrey F. Gardner
Keyword(s):  
Homology Modeling ◽  
Protein Interactions ◽  
Active Site ◽  
Dna Cleavage ◽  
Function Analysis ◽  
Indicator Strain ◽  
Amino Terminal ◽  
Dna Ligation ◽  
Polypeptide Backbone

ABSTRACT CTnDOT integrase (IntDOT) is a member of the tyrosine family of site-specific DNA recombinases. IntDOT is unusual in that it catalyzes recombination between nonidentical sequences. Previous mutational analyses centered on mutants with substitutions of conserved residues in the catalytic (CAT) domain or residues predicted by homology modeling to be close to DNA in the core-binding (CB) domain. That work suggested that a conserved active-site residue (Arg I) of the CAT domain is missing and that some residues in the CB domain are involved in catalysis. Here we used a genetic approach and constructed an Escherichia coli indicator strain to screen for random mutations in IntDOT that disrupt integrative recombination in vivo. Twenty-five IntDOT mutants were isolated and characterized for DNA binding, DNA cleavage, and DNA ligation activities. We found that mutants with substitutions in the amino-terminal (N) domain were catalytically active but defective in forming nucleoprotein complexes, suggesting that they have altered protein-protein interactions or altered interactions with DNA. Replacement of Ala-352 of the CAT domain disrupted DNA cleavage but not DNA ligation, suggesting that Ala-352 may be important for positioning the catalytic tyrosine (Tyr-381) during cleavage. Interestingly, our biochemical data and homology modeling of the CAT domain suggest that Arg-285 is the missing Arg I residue of IntDOT. The predicted position of Arg-285 shows it entering the active site from a position on the polypeptide backbone that is not utilized in other tyrosine recombinases. IntDOT may therefore employ a novel active-site architecture to catalyze recombination.

Phylogenetic relationships of Brazilian bovine respiratory syncytial virus isolates and molecular homology modeling of attachment glycoprotein

2006 ◽  
Vol 116 (1-2) ◽  
pp. 30-37 ◽  
Author(s):  
Fernando Rosado Spilki ◽  
Renata Servan Almeida ◽  
Helena Gallichio Domingues ◽  
Regina Celia Freitas D’Arce ◽  
Helena Lage Ferreira ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Homology Modeling ◽  
Phylogenetic Relationships ◽  
Bovine Respiratory Syncytial Virus ◽  
Syncytial Virus ◽  
Molecular Homology ◽  
Virus Isolates
Sign in / Sign up

Export Citation Format

Share Document