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Resources, Programs and Links for the Fetrow Group and Other Researchers



Related Websites

Computational Biosciences at Wake Forest University
Bioinformatics, Computational Systems Biology, and Computational Biophysics Research and Education at Wake Forest University.

Molecular Signaling Research at Wake Forest University
Molecular signaling research at Wake Forest University ranges from genetic and genomic to protein function, and organismal physiology.

MCODE Network for DC experiment  

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Tools developed by members of the Fetrow Group

PASSS: Protein Active Site Structural Search
Developed by Edward Pryor, PASSS is an implementation of fuzzy functional form descriptors (FFFs; Skolnick and Fetrow, 1998; Fetrow, Godzik and Skolnick, 1998) of active sites in proteins. More information can be found here.

DASP: Deacon Active Site Profiler
Developed by Ryan Huff and Huan Tan, 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. More information can be found here.

SC2ATmd: Standard and Consensus Clustering Analysis Tool for Microarray Data
Developed by Amy Olex, SC2ATmd is a MATLAB-implemented application specifically designed for the exploration of microarray gene expression data via clustering. More information can be found here.

Procavo: PROtein CAVity Observer
Developed by Graham Lopez, PROCAVO can be used to analyze molecular dynamics trajectories to find cavities in proteins and how they change over time. More information can be found here.


In conjunction with the Poole Lab:

PREX: PeroxiRedoxin classification indEX
Developed by Kim Nelson, Laura Soito and Stacy (Knutson) Howerton, PREX is a searchable database of peroxiredoxin protein ids and sequences unambiguously classified into one of six distinct subclasses based on the structural information around the active site. The Deacon Active Site Profiler (DASP) tool was primarly used to populate this database.

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Protein Analysis Tools

Protein function:

Pfam Database
A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

Blocks Database
Protein database of conserved motifs, or blocks. No longer updated, use InterPro database instead.

InterPro Database
A database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.

PRINTS
A database of conserved motifs (fingerprints) used to characterise a protein family.

ProSite
Database of protein domains, families and functional sites.


Other Protein Databases:

IPI - International Protein Index
An EMBL-EBI database that provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms.

PICR - Protein Identifier Cross-Reference Service
A protein ID cross-reference database tool by EMBL-EBI.

Protein structure and structure classification:

CATH
A hierarchical classification of protein domain structures.

SCOP
Structure classification database.

SFLD: Structure-Function Linkage Database
Links evolutionarily related sequences and structures from mechanistically diverse superfamilies of enzymes to their chemical reactions.


Loops in proteins:

SLoop Database (No longer avaliable)
Predicting/identifying loops in proteins.
Click HERE to see the current list of databases provided by the Biochemistry Department at the University of Cambridge.


Protein motions:

MolMovDB
Database that describes the motions that occur in proteins and other macromolecules.


Protein Sequence Analysis:

BLAST
Blast multiple sequence alignment tool.

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Gene Expression Analysis Tools

Clustering analysis tools:

CAGED: Cluster Analysis of Gene Expression Dynamics (No longer publically avaliable)
Cluster analysis software for gene expression data.
Click HERE for more information.

BicAT: Biclustering Analysis Toolbox
Cluster analysis software for gene expression data.

HCE: Hierarchical Clustering Explorer
Interactive exploration of hierarchically clustered data including gene expression data.

MeV: MultiExperiment Viewer
Tools for the analysis of microarray data including statistical analysis, clustering and more.

Statistical analysis and filtering:

SAM: Significance Analysis of Microarrays
MS Excel plugin for the statistical analysis and filtering of microarray data.

GEPAS: Gene Expression Pattern Analysis
Suite of tools for the analysis of microarray data including normalization, preprocessing, filtering, clustering and more.

BioConductor
An open source software project that provides statistical and graphical methods for the analysis of genomic data.


Functional and annotation analysis:

DAVID: Database for Annotation, Visualization and Integrated Discovery
A set of tools for the functional analysis of gene annotations.

G-SESAME: Gene Semantic Similarity Analysis and Measurement Tools
Tools for the semantic analysis of gene annotations.

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Molecular Interaction and Pathway Databases

BioGRID
A general repository for molecular interactions from multiple species.

KEGG
A collection of manually drawn pathway maps representing the current knowledge on molecular interactions and reaction networks.

BioCarta
A pathway database with accompanying analysis tools.

STRING
A database of known protein-protein interactions with an application that integrates interaction data from multiple sources such as literature, experiemntation and genomic context with an intuitive visualization of retrieved networks.

STICH
A project related to STRING. A database that integrates known protein-chemical interactions from various sources with an intuitive visualization of retrieved networks.

BIND
The Biomolecular Interaction Network Database is part of BOND and contains molecular interactions from high-throughput technologies and hand curration of the literature.

IntAct
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

             

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