Tag: Protein

CDTree 3.1 – Protein Domain Hierarchy Viewer and Editor

CDTree 3.1

:: DESCRIPTION

CDTree is a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships;

::DEVELOPER

The NCBI Structure Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

CDTree

:: MORE INFORMATION

Citation:

Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH.
CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.

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

Translate.wdgt – DNA/Protein Conversions

Translate.wdgt

:: DESCRIPTION

Translate.wdgt is for DNA/Protein conversions.

Manipulates DNA or protein sequences.

  • Translate DNA to protein, 3 frames
  • Reverse translate protein to DNA, using human-optimized codons
  • Format (60 characters per line in groups of 10, numbered at line breaks)
  • Scramble
  • Make antiparallel (complementary) strand

::DEVELOPER

Ian York

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOS 10.4 or higher

:: DOWNLOAD

Translate.wdgt

:: MORE INFORMATION

N/A

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.

HMMSTR-CM – Protein Contact Map Prediction

HMMSTR-CM

:: DESCRIPTION

HMMSTR-CM is a software for protein contact map predictions. As above a sequence profile is the input. HMMSTR-CM gives you a JPEG image and text file showing the residues that are most likely to come into contact (distance < 8.0A) in the folded structure. This too is a bare-bones package. This script runs as part of the HMMSTR/Rosetta server.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HMMSTR-CM

:: MORE INFORMATION

Citaiton

Shao Y & Bystroff C. (2003a).
Predicting inter-residue contacts using templates and pathways.
Proteins, Structure, Function and Genetics 53 Suppl 6:497-502.

Bio2MIDI 2.1 – Convert DNA or Protein Sequence to MIDI file

Bio2MIDI 2.1

:: DESCRIPTION

Bio2Midi converts the text of a DNA or protein sequence to a MIDI file, which you may immediately audition, or import into any MIDI sequencer for further compositional processing.

::DEVELOPER

Algorithmic Arts

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Bio2MIDI

:: MORE INFORMATION

N/A

PREFAB 4.0 – Protein Reference Alignment Database

PREFAB 4.0

:: DESCRIPTION

PREFAB (protein reference alignment benchmark) is a database designed for testing multiple sequence alignment methods.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PREFAB

:: MORE INFORMATION

Citation

Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.

REPRO – Protein Repeats Analysis

REPRO

:: DESCRIPTION

REPRO (Protein Repeats Analysis) is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

REPRO

:: MORE INFORMATION

Citation

George RA. and Heringa J. (2000)
The REPRO server: finding protein internal sequence repeats through the web
Trends Biochem. Sci. 25, 515-517.

GAP 1.2.14 – Geometric Analysis of Proteins

GAP 1.2.14

:: DESCRIPTION

GAP (Geometric Analysis Programs)   contains two separate program packages that were developed in parallel for the generation and analysis of structure ensembles.

::DEVELOPER

G.P. Gippert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window with Cygwin / Linux / Mac OsX

:: DOWNLOAD

GAP

:: MORE INFORMATION

DICROPROT 2000 – DICHROism of PROTeins

DICROPROT 2000

:: DESCRIPTION

DICROPROT (DICHROism of PROTeins) was designed to integrate into a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments.

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DICROPROT

:: MORE INFORMATION

Citation:

An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum.
Deléage G, Geourjon C
(1993) Comput Appl Biosci. 2, 197-199.