Gene Regulation Tools Protein Engineering Tools

   

ZLAB has moved to U Mass Medical School in 2008. Dr. Zhiping Weng is now Professor and Director of Program in Bioinformatics and Integrative Biology. Please visit our new ZLAB homepage http://zlab.umassmed.edu. We will continue to host our legacy BU tools here.

 
   

ZLAB stands for "Zhiping's Lab". It has two components: the computational component still needs a catchy name, while the experimental component is called the Protein Engineering Laboratory. Led by Dr. Zhiping Weng, we are a bunch of young people eager to establish careers in Bioinformatics and Biomolecular Engineering. Trying very hard not to be interested in everything, we focus our research on molecular interactions, such as (1) interaction between regulatory proteins and their DNA/RNA target sites (2) protein-protein interaction (3) protein-peptide interaction (4) interaction between protein structure building blocks.


  • SCREEN, Factorbook and other tools as part of the ENCODE Consortium:

    • SCREEN (github): Search Candidate cis-Regulatory Elements by ENCODE.
    • Factorbook: A wiki-based collections of transcription factors with ENCODE ChIP-seq data.
    • LogoJS (github): a Javascript package for creating sequence logos and embedding them in web applications

  • Protein-protein interactions:

    • Docking Benchmark: A large set of test cases for evaluating the performance of docking algorithms
    • ZDOCK: Rigid-body protein-protein docking software, using a fast Fourier transform based search algorithm
    • ZDOCK Conv3D: ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage
    • ZDOCK Server: An automated server for running ZDOCK, with capabilities for blocking and filtering contact residues
    • RDOCK: A refinement method to minimize energy and re-rank ZDOCK predictions
    • ATLAS: The ATLAS database is a manually curated repository containing the binding affinities for TCRs and their antigens

  • Transposon movement in genomic DNA:

    • TEMP2 (github): An algorithm for detecting transposable element movement
    • TEMP: The older version of TEMP2

  • Analysis of deep sequencing data on small RNA pathways:

    • piPipes: A small RNA analysis pipeline 

  • Transcription factor binding:

    • Possum: Simple matrix-based motif search
    • CARRIE: Generate transcriptional regulatory networks from microarray and promoter sequence data
    • Cis-element information: Count matrices and background info for some cis-elements

  • Find clusters of transcription factor binding sites in DNA sequences: 

    • Cluster-Buster (Newest method - our favorite!)
    • Comet (Includes statistical significance estimates)
    • Cister (Our original method)

  • Find diagnostic motifs in a set of regulatory (e.g. promoter or enhancer) sequences:

    • GLAM: Gapless local alignment of multiple sequences (motif discovery)
    • Clover: Find overrepresented motifs in DNA sequences
    • ROVER: Find relatively overrepresented motifs in DNA sequences. New Java Version Available
    • REPFIND: Find clustered, exact repeats in nucleotide sequences
    • MotifViz: Integration of tools for detecting overrepresented motifs
    • SeqVISTA: A viewer of sequences and their annotations with a motif module for integrating transcriptional regulation analysis tools

  • Protein Structure:

    • K2: A genetic algorithm-based protein structure alignment tool
    • FAST: A newer protein structure alignment tool, based on graph theory
    • SMM: A matrix-based algorithm for predicting peptides binding to Major Histocompatibility Complex