These applications and tools described here were developed by students and faculty at Wake Forest University, either as part of research projects or within the context of our interdisciplinary courses.
Identification of protein function is very useful in structural genomics initiatives where the function of a protein structure is not always known in advance of solving the structure. Commonly, the overall protein sequences will be compared and, if similar, the proteins will be assumed to have a similar function. Proteins of similar sequence often exhibit similar functions; however, there are many documented examples where proteins have similar structure and function, but dissimilar sequences. In addition, sequence comparison does not provide information about the chemistry underlying the function. A method was developed to search the three dimensional structure of proteins for structural similarities within their active sites. PASSS is an implementation of fuzzy functional form descriptors (FFFs; Skolnick and Fetrow, 1998; Fetrow, Godzik and Skolnick, 1998) of sites in proteins. Since this application compares the structure, and not sequence, two proteins with similar functional sites, but low overall sequence similarity, will be identified. The tool can be used to extrapolate function from known protein structures to unknown proteins.
For information on PASSS please contact olexal@wfu.edu or edpryor@wfubmc.edu or fetrowjs@wfu.edu.
Tools that allow detailed characterization of functional site features in proteins of known structure are much needed. DASP is a web site application that implements a previously described method (Cammer, et al., 2003) and allows users to create a functional site profile for any protein family. Two protocols for functional site analysis of protein families using DASP have been described (Fetrow, 2006): 1) Protocol 1, creation of functional site signatures and a profile from proteins of known structure and 2) Protocol 2, utilization of the active site profile to search sequences that contain fragments similar to those found in the functional site signatures. The active site profile produced by Protocol 1 allows the user to analyze the features of the functional site, i.e., those characteristics that are common across the family and those that are unique to one or several members of the family. The characteristics that are unique to a subfamily might be described as specificity determinants, i.e., features that impart specificity to a particular function. Protocol 2 provides instructions for searching for sequences that might contain a similar functional site.
User's Manual
Go to DASP homepage
For more information on DASP please contact olexal@wfu.edu or fetrowjs@wfu.edu
SC2ATmd is a MATLAB-implemented application specifically designed for the exploration of microarray gene expression data via clustering. Implementation of two versions of the "figure of merit" (FOM) clustering validation method allows for performance comparisons between different clustering algorithms, and tailors the cluster analysis process to the varying characteristics of each data set. Along with standard clustering algorithms this application also offers a consensus clustering method that can generate reproducible clusters across replicate experiments and different clustering algorithms. This application was designed specifically for the analysis of gene expression data, but may be used with any numerical data.
SC2ATmd may be freely downloaded from the links below. Two versions of the application are avaliable: a stand-alone Windows application and the Matlab source code. The Matlab Source Code Package allows user's to run SC2ATmd on any OS that has a fully licensed version of Matlab. For those who do not have Matlab, a stand-alone Windows executable is provided. The stand-alone Windows executable requires that Matlab Component Runtime v72 (MCRv72 is freely avaliable) be installed prior to SC2ATmd. If you already have MCRv72 installed on your machine you may download the partial SC2ATmd package which does not include MCR, otherwise you must download the full package. For all packages, save and unzip the .zip or .tgz file to your computer in the location that you want the application to execute from. Follow the included installation instructions to install and run SC2ATmd.
SC2ATmd is released under the GNU GPLv3 license and may be freely used, modified and distributed as needed.
For more information on SC2ATmd please contact olexal@wfu.edu or fetrowjs@wfu.edu
Molecular dynamics is a common tool to explore the time-based characteristics of protein structure. However, it can be difficult to explore the evolution in time of specific structural features like cavities. PROCAVO can be used to analyze molecular dynamics trajectories to find cavities in proteins and how they change over time. This is done by marking the cavities in the protein for every frame of the MD trajectory, then summarizing these results in a way that tells the user about the behavior of the cavity space over a period of time. After the cavity marking, PROCAVO uses modular analysis programs to help the user visualize specific features of the dynamic cavity space using VMD. Procavo is released under the GNU GPLv3 lisence and was designed to run on Linux. PROCAVO is avaliable as a .gz file here (right click and select 'Save As'), and installation instructions and the user's manual in PDF format are here.
For more information on Procavo please contact lopemg6@wfu.edu or fetrowjs@wfu.edu
Site-MAPS is a web-service application designed to assist users in finding statistically significant nucleotide motifs in non-coding regions of genomic sequences. The core of Site-MAPS is built around the use of the probabilistic suffix tree data-structure and corresponding algorithms for selecting a set of sequences that are within user defined length parameters, non-random in makeup, and present in non-trivial numbers to use as candidate motifs. These candidate motifs can then be evaluated under two different scoring mechanisms for statistical significance: 1) a sequence-derived scoring mechanism where expected usage rates are based on the nucleotide distribution of both the motif and the sequences searched and 2) a binomial-distribution scoring mechanism where the expectation is computed from a previously generated database of promoter sequences of similar length and from the same genome.
Site-MAPS is designed to support motif analysis for genes in the Mus musculus (mouse) and Saccharomyces cervisiae (Baker’s yeast) genomes, with it’s interface designed so that users only need to submit gene names or IDs of clusters of genes of interest for analysis. Because Site-MAPS is a web application, it only requires an up-to-date web browser to run. A user’s manual will be available shortly.
For informationon GeneWork please contact turketwh@wfu.edu or fyejm5@wfu.edu.
Furball is a tool for the analysis of protein interaction networks. The program allows for a set of target proteins to be identified within the program for comparison against the network as a whole. Furball employs a series of graphs and statistics to provide visual and quantitative data to better understand the target proteins as compared to the entire network. Released under the GNU GPLv3 license, Furball is free to use, modify and distribute as you see fit. Furball can be integrated into the classroom as well as laboratrory work. Documentation and a user manual are provided on the Documents page.
Furball was designed by a group of Biology and Computer Science students at Wake Forest University.
User's Manual
Go to FurBall homepage
For more information on FurBall please contact turketwh@wfu.edu
