Category: Protein Sequence Analysis

PexSPAM 1.2 – Protein Sequence Feature Extraction

PexSPAM 1.2

:: DESCRIPTION

PexSPAM is a Java standalone program that I wrote for protein sequence feature extraction. PexSPAM was originally designed to be a “feature factory” for secondary structure classification problem in integral membrane proteins. PexSPAM extends the SPAM (Ayres et al, 2002) method by incorporating gap and regular expression constraints into mining procedure.

::DEVELOPER

Joshua Ho

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix
  • Java

:: DOWNLOAD

 PexSPAM for Win , Source Code

:: MORE INFORMATION

Citation:

Ho J, Lukov L, Chawla S (2005)
Sequential Pattern Mining with Constraints on Large Protein Databases.
In Chakrabarti S, Sudarshan S, Radha Krishnan P (Eds) Proceedings of the 12th International Conference on Management of Data (COMAD 2005b), 89-100.

DomainFinder 2.0.4 – Determine Dynamical Domains in Protein

DomainFinder 2.0.4

:: DESCRIPTION

DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are

  1. computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes
  2. ease of use: a state-of-the-art graphical user interface
  3. export of results for visualization and further analysis (VRML, PDB, and MMTK object format)

::DEVELOPER

Konrad Hinsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DomainFinder

:: MORE INFORMATION

Citation:

K. Hinsen
Analysis of domain motions by approximate normal mode calculations
Proteins 33(3), 417-429 (1998)

ProCope 1.2 – Protein Complex Prediction and Evaluation

ProCope 1.2

:: DESCRIPTION

ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

ProCope

:: MORE INFORMATION

Citation

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer.
ProCope–protein complex prediction and evaluation.
Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.

ProteinVis 2.1.6 – Tree viewer for Hierarchical Clusterings of Proteins

ProteinVis 2.1.6

:: DESCRIPTION

ProteinVis is a tree viewer for hierarchical clusterings of proteins in the human Genome.Many genomic and proteomic analyses generate as a result a tree of genes or proteins. These trees are often large (containing tens of thousands of nodes and edges), and need a visualization tool to fully display all the information contained in the tree. Clustering analysis can be performed on these trees to obtain clusters of proteins, and we need an efficient way to visualize the clustering results. We present a novel tree visualization tool to help with such analyses.

::DEVELOPER

Jefferson Robert Heard ; Xiaojun Guan, and a professor of biology at UNC Chapel Hill, Dr William Kaufman.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

ProteinVis for win ; for Linux

:: MORE INFORMATION

Citation

Jeff Heard1,, William Kaufmann and Xiaojun Guan1,
A novel method for large tree visualization
Bioinformatics (2009) 25 (4): 557-558.

ProTag 1.4 – Office Add-In for offering SmartTag of Protein

ProTag 1.4

:: DESCRIPTION

ProTag is a SmartTag and Add-In solution for the Microsoft Office applications Word, Excel and PowerPoint. It recognizes the names and (database) identifiers of proteins within free text and offers the user to perform different actions on the protein, e.g. to show all synonyms.

::DEVELOPER

Teaching and Research Unit Bioinformatics from the Department of Informatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MS Office

:: DOWNLOAD

ProTag

:: MORE INFORMATION

Citation

Szugat,M., Güttler,D., Fundel,K., Sohler,F., Zimmer,R.,
Web servicing the biological office,
Bioinformatics, ECCB/JBI, Vol. 21 Suppl. 2 2005, pages ii268-ii269

STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam

STORM 1.01

:: DESCRIPTION

STORM (Systematic Tailored Orf-data Retrieval & Management) combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format.More specifically, STORM extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties.

::DEVELOPER

Laboratory of Gene Technology, Katholieke Universiteit Leuven

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Access

:: DOWNLOAD

STORM

:: MORE INFORMATION

Citation

Lavigne, R., Sun, W.D. and Volckaert, G.
STORM towards protein function: Systematic Tailored ORF-data Retrieval and Managment.
Applied Bioinformatics (2003) 2(3): 177-179

MPtopoQuerier – Search Database of Membrane Proteins

MPtopoQuerier

:: DESCRIPTION

MPtopoQuerier is a java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.

::DEVELOPER

Stephen White laboratory at UC Irvine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

MPtopoQuerier

:: MORE INFORMATION

Citation

Jayasinghe, S., Hristova, K., and White, S. H. (2001).
MPtopo: A database of membrane protein topology.
Protein Sci 10:455-458.

MPEx 3.2 – Tool for Exploring Membrane Proteins

MPEx 3.2

:: DESCRIPTION

MPEx (Membrane Protein Explorer) is a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles.

::DEVELOPER

Stephen White laboratory at UC Irvine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

MPEx

:: MORE INFORMATION

Citation

Snider C, Jayasinghe S, Hristova K, & White SH (2009).
MPEx: A tool for exploring membrane proteins.
Protein Sci 18:2624-2628. [PubMed Abstract].

I-sites 2 – Predict the Local Structure of a Protein

I-sites 2

:: DESCRIPTION

I-sites is a method for predicting initiation sites of folding protein sequences.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

I-sites

:: MORE INFORMATION

Citaiton

Bystroff C & Baker D. (1998).
Prediction of local structure in proteins using a library of sequence-structure motifs.
J Mol Biol 281, 565-77.

PROTEAN – Torsion Space Molecular Simulations

PROTEAN

:: DESCRIPTION

PROTEAN is a set of Fortran subroutines for calculating the equations ofmotion in torsion space for polypeptides. Torsion space is the space of all rotatable bonds. Bond lengths and bond angles remain fixed at their ideal values in a torsion space simulation. Simulations in torsion space are at least ten times more efficient than simulations in Cartesian space.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PROTEAN

:: MORE INFORMATION

Citaiton

Bystroff, C. (2001)
An alternative derivation of the equations of motion in torsion space for a branched linear chain.
Protein Engineering 14, 825-828.