Tag: SPIDER

SpideR 1.5.0 – SPecies IDentity and Evolution in R

SpideR 1.5.0

:: DESCRIPTION

Spider is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation.

::DEVELOPER

SpideR team

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 SpideR

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2012 May;12(3):562-5. doi: 10.1111/j.1755-0998.2011.03108.x. Epub 2012 Jan 16.
Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.
Brown SD1, Collins RA, Boyer S, Lefort MC, Malumbres-Olarte J, Vink CJ, Cruickshank RH.

SPIDER 26.06 – Image processing system for Electron Microscopy

SPIDER 26.06

:: DESCRIPTION

SPIDER (System for Processing Image Data in Electron microscopy and Related fields) is an image processing system for electron microscopy, especially usefull for single-particle reconstruction.

::DEVELOPER

Wadsworth Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPIDER

:: MORE INFORMATION

Citation

Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J.
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
Nat Protoc. 2008;3(12):1941-74. doi: 10.1038/nprot.2008.156. PMID: 19180078; PMCID: PMC2737740.

SPIDER – Scoring Protein Interaction Decoys using Exposed Residues

SPIDER

:: DESCRIPTION

SPIDER is developed as a knowledge-based scoring function for protein-protein interaction decoys. SPIDER is a novel multi-body pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. SPIDER’s score relies on the geometric similarity of interfacial residues between docking poses and naturally occuring (native) poses.

::DEVELOPER

SPIDER Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPIDER

:: MORE INFORMATION

Citation

Raed Khashan, Weifan Zheng, and Alexander Tropsha.
Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.
Proteins: Structure, Function, and Bioinformatics, Volume 80, Issue 9, Pages 2207-2217, August 2012.