Tuesday, 28 February 2012

Jinjiang's WebWatcher on Biology (5) - protein-protein docking tools

Web based tools
 • PREPPI: A web service to predict protein-protein interactions by combining structural and non-structural information.
 • PredUs: A tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors.
 • PUDGE: This protein structure prediction server provides a convenient means of integrating tools that may be used at different stages of the structural prediction process.
 • Mark-Us: A Function Annotation Server for Protein Structures.
 • Target Explorer: A web based tool for automatic identification of new target genes for transcription factors in the Drosophila genome.
 • EDGI: (Enhancer Detection using only Genomic Information) discovers transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting.
 • Model Quality Assessment: Global and Local Quality Assessment of Protein Models.
 • STING Millennium: A web based suite of programs for comprehensive and simultaneous analysis of structure and sequence: nature and volume of atomic contacts of both intra- and inter- chain types, analysis of the quality of structure, residue conservation and its relationship with intra-chain contacts, functional parameters are also deciphered.
 • SCREEN: A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
 • RoettaDock server at http://rosettadock.graylab.jhu.edu/
 • HADDOCK at http://haddock.science.uu.nl
 • Cluspro 2.0 (with antibody mode):http://cluspro.bu.edu/login.php
 •  HEX 6.3: http://hex.loria.fr
 • GRAMMX (Vakser Tool) online or ZDOCK
 • prediction tools for interfaces - CPORT;  http://haddock.science.uu.nl/services/CPORT
 • Vina http://vina.scripps.edu/
 •  PS2 http://ps2.life.nctu.edu.tw/

 • STRAP java,  for comparing multiple PDB and visualisation 3D structure
--  http://www.charite.de/bioinf/strap/Scripting.html
 • BALLView -- http://www.ball-project.org/Ballview
 • Structural Analysis and Verification Server: http://nihserver.mbi.ucla.edu/SAVES/
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Friday, 24 February 2012

Jinjiang's WebWatcher on Biology (4) - Protein-DNA databases


Protein-DNA binding databases (TF-DNA & ligand-DNA; excluding histone-DNA):
This is just the paper; the web interface for the database is not available yet (28.12.2011).
FlyTF currently contains 129 proteins for which PWMs are available.
TRANSFAC consists of free and paid sections. Provided binding sites are experimentally proved. Human TF weight matrices may be viewed through the web interface of UCSC Genome Browser.
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference from TRANSFAC is the open access to the data.
KDBI is a collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding events described in the literature.
ProNIT currently contains more than 4900 entries. Each entry has the protein and nucleic acid information, experimental conditions and the following binding thermodynamic data: dissociation constant Kd, energies, stoichiometry of binding and activity (Km and kcat).
UniPROBE contains data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 391 nonredundant proteins (individual proteins or in some cases heterodimers) from a diverse collection of organisms.
This is a personal collection. Currently contains ~50 matrices (Last checked: 06.10.2010).

Calculating TF affinity (binding constant) from weight matrices and directly from experiments:*
TRAP calculates binding affinity based on the matrix description of a given TF and a set of DNA sequences to be annotated (input). It requires the specification of two biophysically-motivated parameters. The freely available program code is written in C. Further details are available in the paper by Roider et al., 2007.
STAP uses a biophysical model to analyzes transcription factor (TF)-DNA binding data, such as ChIP-chip or ChIPSeq data. The program assumes that the measured affinity of a sequence to a TF (TF_exp) in some ChIP-chip or ChIP-seq experiment is determined by: 1) the number and strength of binding sites of TF_exp in this sequence; 2) the presence of other sites that may interact cooperatively with the sites of TF_exp in the neighborhood. Specifically, it takes as input a set of DNA sequences, their binding affinities to some TF as measured by experiments (TF_exp), and the position weight matrices (PWMs) of a set of TFs, including TF_exp. It will learn the relevant parameters of the biophysical model of TF-DNA interaction, including those of TF-DNA interaction and those of TF-TF cooperative interactions. **To be tested.
    The input to MatrixREDUCE is a sequence file in FASTA format and an expression data file in tab-delimited text format (missing values are allowed). Output data include PSAMs in numeric and graphical format, parameters of the fitted model, and an HTML summary page.
    BayesPI integrates Bayesian model regularization with biophysical modeling of protein-DNA interactions and nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. **To be tested.
    The scoring function calibrated against crystallographic data on protein-DNA contacts can recover PWMs, sometimes outperforming experimental PWMs. **To be tested
    *Section under construction. Check again later and feel free to submit your links and comments

    General-purpose numbers relevant for gene regulation:
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    Monday, 20 February 2012

    Jinjiang's WebWatcher on Biology (3) - Free statistics

    VassarStats: Website for Statistical Computation
    http://vassarstats.net/
    WinPEPI
    http://www.brixtonhealth.com/pepi4windows.html
    RExcel
    http://rcom.univie.ac.at/

    Statistical Calculators - General


    Statistical Calculators - Specific Procedures



    Useful Sites for Specific Software Programs



    Access



    Excel




    Pivot Tables


    SAS



    STATA



    SPSS


    References/Resources



    Specific Procedures



    Syntax



    Tutorials



    Utilities


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    Jinjiang's WebWatcher on Biology (2) - FREE Deconvolution software

    FREE Deconvolution software
    ref: http://deconvolve.net/DNLinks.html
    • ImageJ A Java-based image processing platform from the NIH (US). Can accept many plug-ins including deconvolution, some of which are listed below.
    • Iterative Deconvolution Iterative Deconvolution in 2D for ImageJ by Bob Dougherty.
    • Iterative Deconvolve 3D Iterative Deconvolution in 3D for ImageJ by Bob Dougherty.
    • Deconvolution Spectral/Iterative/HRRT Deconvolution in 2D and 3D for ImageJ by Piotr Wendykier.
    • Colour Deconvolution Colour deconvolution of Ruifrok and Johnston ('stain separation' or 'spectral unmixing') as implemented by G. Landini for ImageJ. If you use this, why not consider comparing your results to those obtainable with the BiaQIm IP Suite programs StainSep and SpecSep?
    • DeconvolutionJ An ImageJ plugin that implements deconvolution based on a Regularized Wiener Filter by Nick Linnenbrügger.
    • Image Surfer A free 3D imaging suite to visualize and analyze multi-channel volumes. This uses the free Clarity Deconvolution C/C++ library from the University of North Carolina.
    • Motion Deblur Image deblurring by a novel algorithm by Qi Shan, Jiaya Jia and Aseem Agarwala of The Chinese University of Hong Kong.
    • UnShake Blind deconvolution of photos affected by poor-focus or camera-shake by M.D. Cahill.
    • IRIS Astronomical image processing software by Christian Buil. Implements Lucy-Richardson, van Cittert and maximum entropy deconvolution as well as many other processes.
    • GRIP Software by Graham Relf. Implements van Cittert deconvolution as well as many other processes.
    • LASIP Blind Frequency domain blind deconvolution in multiframe imaging using anisotropic spatially-adaptive denoising for MATLAB version 6.5 or later from the Tampere University of Technology, Finland.
    • UnBLur A deconvolution program (claimed to be applicable for images of arbitrary dimensionality) by John Costella.
    • Deconv This link is to an article abstract describing the software: Sun Y, Davis P, Kosmacek EA, Ianzini F, Mackey MA. An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging. J Microsc. 2009 Dec; 236(3):180-93.
    • TriaDemo Tria is a program by Dr James Caron of Quarktet and incorporates the SeDDaRA deconvolution algorithm. The demo version is free but has save functions disabled.
    • SAR The SAR Image processor has least squares and least absolute deviation methods implenented by Steven A. Ruzinsky. The free version is limited by having save and print functions disabled.
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