Bodil statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

Bodil specifications

Information


Unique identifier OMICS_17133
Name Bodil
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Medium
Stability Beta
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Mark Johnson

Additional information


Different versions of Bodil are available at http://users.abo.fi/bodil/download.php.

Publication for Bodil

Bodil citations

 (33)
library_books

Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana

2018
Sci Rep
PMCID: 5953924
PMID: 29765071
DOI: 10.1038/s41598-018-25872-0

[…] 1A offered a plausible template for homology modelling of different Gs1l transcripts. Next, the sequence alignments of all the transcripts and the crystal structure of HDHD1A were made with Malign in Bodil Modeling Environment by employing structure-based matrix (STRMAT110) with gap formation penalty of 60. Based on formed sequence alignment, models of transcripts were built with Modeller v9.16. […]

library_books

Improving Docking Performance Using Negative Image Based Rescoring

2018
Front Pharmacol
PMCID: 5879118
PMID: 29632488
DOI: 10.3389/fphar.2018.00260

[…] h the docking and rescoring could work better or worse using different structures. The necessary PDB entry editing (Figure ) such as the removal of bound ligands from the active sites was done in the BODIL Molecular Modeling Environment (Lehtonen et al., ). The protein residues were protonated with the default settings in REDUCE3.24 (Word et al., ). The X-ray crystal structure waters were left in […]

call_split

Structure Activity Relationship Analysis of 3 Phenylcoumarin Based Monoamine Oxidase B Inhibitors

2018
PMCID: 5840146
PMID: 29552556
DOI: 10.3389/fchem.2018.00041
call_split See protocol

[…] henylcoumarin scaffold and the 24 most potent inhibitor derivatives shown in Figures , 2 were drawn with BIOVIA DRAW 2016 (Dassault Systèmes, San Diego, CA, USA, 2016). Figures , were prepared using BODIL (Lehtonen et al., ) and VMD 1.9.2 (Humphrey et al., ). The negative images of the MAO-B and MAO-A binding cavities shown in Figure and C were outlined using PANTHER (Niinivehmas et al., , ) and […]

library_books

Mapping the interaction site and effect of the Siglec 9 inflammatory biomarker on human primary amine oxidase

2018
Sci Rep
PMCID: 5794975
PMID: 29391504
DOI: 10.1038/s41598-018-20618-4

[…] tKB and sequences pig (Sus scrofa) (ID: XP_020922632.1) and rabbit (Oryctolagus cuniculus) (ID: XP_002719460.1) from NCBI (www.ncbi.nlm.nih.gov). These sequences were aligned using the MALIGN tool in BODIL. […]

call_split

Joint inflammation related citrullination of functional arginines in extracellular proteins

2017
Sci Rep
PMCID: 5557964
PMID: 28811641
DOI: 10.1038/s41598-017-08597-4
call_split See protocol

[…] Protein structures were obtained from the Protein Data Bank (PDB). Structures were visualized and figures of structures prepared using Bodil. Sequences surrounding arginine residues found to be citrullinated were obtained from the structure file when available, and from the UniProt database.The peptides NGR and isoDGR were built usin […]

library_books

Skeletal Dysplasia Mutations Effect on Human Filamins’ Structure and Mechanosensing

2017
Sci Rep
PMCID: 5484675
PMID: 28652603
DOI: 10.1038/s41598-017-04441-x

[…] n be identified with protein names (filamin-a/filamin-b), have more than 2,000 residues, and are available for both FLNa and FLNb. The resulting 19 sequences for both FLNs were aligned with Malign in Bodil by using Structure-based matrix with gap penalty of 90. The high gap penalty ensures that in the case of inserted/deleted domains, the gaps are not spread between nearby domains. The Supplementa […]

Citations

Looking to check out a full list of citations?

Bodil institution(s)
Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistokatu, Turku, Finland; Department of Mathematics, University of Turku, Matematiikan laitos, Turun yliopisto, Finland; CSC, the Finnish IT Center for Science, Espoo, Finland
Bodil funding source(s)
Supported by TEKES – the National Technology Agency of Finland, the Academy of Finland, the Ministry of Education, the Foundation of Abo Akademi University, the Erna and Victor Hasselblad Foundation (Sweden), the Sigfrid Juselius Foundation, the Tor, Joe och Pentti Borgs minnesfund, Fatman Bioinformational Designs Ltd, the National Graduate School in Informational and Structural Biochemistry, Finland, and the Graduate School in Computational Biology, Bioinformatics and Biometry, Finland.

Bodil reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Bodil