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

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

:: 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.

PINES – Phenotype-Informed Noncoding Element Scoring

PINES

:: DESCRIPTION

PINES evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
R

:: DOWNLOAD

PINES

:: MORE INFORMATION

Citation

Bodea CA, Mitchell AA, Bloemendal A, Day-Williams AG, Runz H, Sunyaev SR.
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.
Genome Biol. 2018 Oct 25;19(1):173. doi: 10.1186/s13059-018-1546-6. PMID: 30359302; PMCID: PMC6203199.

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

Research and Information Systems

:: 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.

DAS tool 1.1.3 – Recovery of Genomes from Metagenomes via Dereplication, Aggregation, and Scoring Strategy

DAS tool 1.1.3

:: DESCRIPTION

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

DAS Tool

:: MORE INFORMATION

Citation

Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF.
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.
Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28. PMID: 29807988; PMCID: PMC6786971.

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 Lab

:: 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.

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

:: 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