ModPipe 2.3.0 – Calculate Protein Structure Model

ModPipe 2.3.0

:: DESCRIPTION

ModPipe is a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention. In the simplest case, it takes as input a sequence identifier and a configuration file and produces one or more comparative models for that sequence.

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ModPipe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. Epub 2010 Nov 19.
ModBase, a database of annotated comparative protein structure models, and associated resources.
Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sj?lander K, Ferrin TE, Burley SK, Sali A.

Spatial 1.0.0 – Model Animal Movement on Landscapes

Spatial 1.0.0

:: DESCRIPTION

Spatial is an agent-based model of the movements of animals on landscapes. The landscapes can be entered from image files or from tables of data. Rules are entered to describe the attractiveness, permeability, and rate of movement of animals for each landscape feature (optionally including other animals). Spatial then simulates the movements over time, and dsiplays final location, tracks, or density of occupancy.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Spatial 

:: MORE INFORMATION

MAINMAST 1.0 – MAINchain Model trAcing using Spanning Tree from a EM map

MAINMAST 1.0

:: 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

MAINMAST

:: 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.

MARRVEL v2 – Model organism Aggregated Resources for Rare Variant ExpLoration

MARRVEL v2

:: DESCRIPTION

MARRVEL aims to facilitate the use of public genetic resources to prioritize rare human gene variants for study in model organisms. To automate the search process and gather all the data in a simple display we extract data from human data bases (OMIM, ExAC, Geno2MP, DGV, and DECIPHER) for efficient variant prioritization. The protein sequences for six organisms (S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens) are aligned with highlighted protein domain information via collaboration with DIOPT.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE; UDN, Perrimon N, Liu Z, Bellen HJ.
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Am J Hum Genet. 2017 Jun 1;100(6):843-853. doi: 10.1016/j.ajhg.2017.04.010. Epub 2017 May 11. PMID: 28502612; PMCID: PMC5670038.

Camelot – Model Complex Traits and Identify the Potential underlying Causal Factors

Camelot

:: DESCRIPTION

Camelot (CAusal Modeling with Expression Linkage for cOmplex Traits) is a statistical method that integrates genotype, gene expression and phenotype data to automatically build models that both predict complex quantitative phenotypes and identify genes that actively influence these traits.

::DEVELOPER

Dana Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MatLab

:: DOWNLOAD

Camelot

:: MORE INFORMATION

Citation

Mol Syst Biol. 2009;5:310. doi: 10.1038/msb.2009.69.
Harnessing gene expression to identify the genetic basis of drug resistance.
Chen BJ, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe’er D.

Piet 0.1.0 – DNA CNV Analysis tools based on fused Lasso type of Model

Piet 0.1.0

:: DESCRIPTION

Piet provides some segmentation tools, using fused lasso, group fused lasso and generalized fused lasso (GFL), for analysis of individual or multiple sequences of CNV data.

::DEVELOPER

Piet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • R package

:: DOWNLOAD

 Piet

:: MORE INFORMATION

Citation

Z. Zhang, K. Lange, C. Sabatti (2012)
Reconstructing DNA copy number by joint segmentation of multiple sequences

bnpsd 1.2.3 – Model and Simulate Admixed Populations

bnpsd 1.2.3

:: DESCRIPTION

bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

bnpsd

:: 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.

CreateFibril 2.5 – Build Atomic Resolution Models of Protein Fibrils

CreateFibril 2.5

:: DESCRIPTION

CreateFibril is a tool to build atomic resolution models of protein fibrils.

::DEVELOPER

CreateFibril team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CreateFibril

:: 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.

SOMPNN – An Efficient Non-Parametric Model for Predicting Transmembrane Helices

SOMPNN

:: DESCRIPTION

SOMPNN is a novel model for prediction of TMH that features by minimal parameter assumptions requirement and high computational efficiency. In the SOMPNN model, a self-organizing map (SOM) is used to adaptively learn the helices distribution knowledge hidden in the training data, and then a probabilistic neural network (PNN) is adopted to predict TMH segments based on the knowledge learned by SOM.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

  SOMPNN 

 :: MORE INFORMATION

Citation:

Amino Acids. 2012 Jun;42(6):2195-205. doi: 10.1007/s00726-011-0959-2. Epub 2011 Jun 22.
SOMPNN: an efficient non-parametric model for predicting transmembrane helices.
Yu DJ1, Shen HB, Yang JY.

BMIQ 1.4 – Beta Mixture Quantile Model

BMIQ 1.4

:: DESCRIPTION

BMIQ (Beta Mixture Quantile) is a method for normalisation of Illumina Infinium 450k data

::DEVELOPER

Teschendorff Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 BMIQ 

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):189-96. doi: 10.1093/bioinformatics/bts680. Epub 2012 Nov 21.
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Teschendorff AE1, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S.