NEST 1.0 – Network Essentiality Scoring Tool

NEST 1.0

:: DESCRIPTION

The NEST is designed to predict the gene essentiality based on protein interaction network and gene expression or CRISPR screen results.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 NEST

:: MORE INFORMATION

Citation

Network analysis of gene essentiality in functional genomics experiments.
Jiang P, Wang H, Li W, Zang C, Li B, Wong YJ, Meyer C, Liu JS, Aster JC, Liu XS.
Genome Biol. 2015 Oct 30;16:239. doi: 10.1186/s13059-015-0808-9.

SPRINT – Scoring PRotein INTeractions

SPRINT

:: DESCRIPTION

SPRINT is a C++/OpenMP program that predicts protein-protein interactions.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPRINT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Nov 15;18(1):485. doi: 10.1186/s12859-017-1871-x.
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.
Li Y, Ilie L

STRIKE 1.2 – Sequence Alignment Scoring Tool

STRIKE 1.2

:: DESCRIPTION

STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  STRIKE

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.
STRIKE: evaluation of protein MSAs using a single 3D structure.
Kemena C, Taly JF, Kleinjung J, Notredame C.

ASSIsT 1.02 – Automated SNP Scoring Tool

ASSIsT  1.02

:: DESCRIPTION

ASSIsT is a tool for the efficient filtering of Illumina Infinium/BeadExpress based SNP markers.

::DEVELOPER

the Computational Biology Center for the community of researchers at FEM

:: SCREENSHOTS

ASSIsT

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ASSIsT

:: MORE INFORMATION

Citation:

ASSIsT: An Automatic SNP ScorIng Tool for in- and outbreeding species.
Di Guardo M, Micheletti D, Bianco L, Koehorst-van Putten HJ, Longhi S, Costa F, Aranzana MJ, Velasco R, Arús P, Troggio M, van de Weg EW.
Bioinformatics. 2015 Aug 6. pii: btv446

Seder 2.0 – A Global Protein Structure Scoring Function

Seder 2.0

:: DESCRIPTION

Seder is a protein scoring function. The package was designed using the GEneral Neural Network program.

::DEVELOPER

Battelle Center for Mathematical Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • SAS
  • Perl
  • C/C++ Compiler
  • FORTRAN (77/90/etc.)

:: DOWNLOAD

 Seder

:: MORE INFORMATION

Citation

A global machine learning based scoring function for protein structure prediction.
Faraggi E, Kloczkowski A.
Proteins. 2014 May;82(5):752-9. doi: 10.1002/prot.24454. Epub 2013 Nov 22.

Dispec – Peptide Scoring Algorithm Based on Peptide Matching Discriminability

Dispec

:: DESCRIPTION

Dispec is a database searching algorithm to identify peptides from tandem mass spectrometry (MS/MS) based on Discriminating Labled Spectra for candidate peptides

::DEVELOPER

Proteomics Research Group in Jinan University

:: SCREENSHOTS

Dispec

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 Dispec

:: MORE INFORMATION

Citation

PLoS One. 2013 May 13;8(5):e62724. doi: 10.1371/journal.pone.0062724. Print 2013.
Dispec: a novel peptide scoring algorithm based on peptide matching discriminability.
Xiao CL1, Chen XZ, Du YL, Li ZF, Wei L, Zhang G, He QY.

pyDockWEB – Rigid-body docking and scoring by pyDock

pyDockWEB

:: DESCRIPTION

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm

::DEVELOPER

Protein Interactions and Docking Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):1698-9. doi: 10.1093/bioinformatics/btt262. Epub 2013 May 9.
pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
Jiménez-García B1, Pons C, Fernández-Recio J.

G-NEST – Gene Neighborhood Scoring tool

G-NEST

:: DESCRIPTION

G-NEST combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes.

::DEVELOPER

Pollard Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 G-NEST

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 28;13:253. doi: 10.1186/1471-2105-13-253.
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.
Lemay DG1, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS.

CSS-Palm 4.0 – Palmitoylation Site Prediction with a Clustering and Scoring Strategy

CSS-Palm 4.0

:: DESCRIPTION

CSS-Palm is a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction.The program’s prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6).

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 CSS-Palm

:: MORE INFORMATION

Citation

CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Jian Ren, Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao.
Protein Engineering, Design and Selection.2008 21(11):639-644

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.