:: DESCRIPTION
MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.
Terashi G, Kihara D.
J Struct Biol. 2018 Nov;204(2):351-359. doi: 10.1016/j.jsb.2018.07.013.
:: DESCRIPTION
bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ochoa, Alejandro, and John D. Storey. 2016a.
“FST And Kinship for Arbitrary Population Structures I: Generalized Definitions.”
bioRxiv doi:10.1101/083915.
Ochoa, Alejandro, and John D. Storey. 2016b.
“FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.”
bioRxiv doi:10.1101/083923.
:: DESCRIPTION
Path2Models automatically generates mathematical models from biological pathway representations using a suite of freely available software. Computed models from over 2600 organisms encoded in SBML and SBGN are available through the BioModels Database.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, et al.
BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.
:: DESCRIPTION
MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes.
::DEVELOPER
Network Biomedicine Laboratory at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
Hwang S, Kim E, Yang S, Marcotte EM, Lee I.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434.
:: DESCRIPTION
PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Matsui, H, Sato, K. and Sakakibara, Y.,
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures,
Bioinformatics, vol.21, no.11, pp.2611-2617, 2005
:: DESCRIPTION
CreateFibril is a tool to build atomic resolution models of protein fibrils.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biophys J. 2013 Feb 5;104(3):683-93. doi: 10.1016/j.bpj.2012.12.037.
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.
Smaoui MR1, Poitevin F, Delarue M, Koehl P, Orland H, Waldispühl J.
:: DESCRIPTION
MICC is an R package which provides methods to detect chromatin interactions from ChIA-PET data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MICC: an R package for identifying chromatin interactions from ChIA-PET data.
He C, Zhang MQ, Wang X.
Bioinformatics. 2015 Jul 31. pii: btv445.
:: DESCRIPTION
BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).
::DEVELOPER
The RNA-Informatics Research Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.
:: DESCRIPTION
MEED is a tool for practical microarray experimental design that can suggest experiments so as to avoid ambiguity in the identification of regulatory relatrionships.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Szczurek E, Gat-Viks I, Tiuryn J, Vingron M:
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.
Mol Syst Biol 2009, 5:287.
:: DESCRIPTION
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
CellDesigner is free to use >> License text
