SIfTER 2015 – Mapping Protein Conformation Spaces

SIfTER 2015

:: DESCRIPTION

SIfTER is a structure-guided memetic, cellular, and multiscale evolutionary algorithm for mapping protein conformation spaces. It is based instead on stochastic optimization to circumvent the computational challenge of exploring the breadth of a protein’s structure space.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SIfTER

:: MORE INFORMATION

Citation

Clausen R, Ma B, Nussinov R, Shehu A.
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.
PLoS Comput Biol. 2015 Sep 1;11(9):e1004470. doi: 10.1371/journal.pcbi.1004470. PMID: 26325505; PMCID: PMC4556523.

Sifter-T 1.2.1 – Optimized Framework for SIFTER Phylogenomic method

Sifter-T 1.2.1

:: DESCRIPTION

SIFTER-T (SIFTER Throughput-optimized), a substantial improvement over SIFTER’s original proof-of-principle implementation. SIFTER-T is optimized for better performance, allowing it to be used at the genome-wide scale.

::DEVELOPER

The Laboratory for Biological Information Processing – LabPIB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

Sifter-T

:: MORE INFORMATION

Citation:

Biotechniques. 2015 Mar 1;58(3):140-2. doi: 10.2144/000114266. eCollection 2015.
SIFTER-T: A scalable and optimized framework for the SIFTER phylogenomic method of probabilistic protein domain annotation.
Almeida-E-Silva DC, Vêncio RZ

SIFTER 2.1.1 – Genome-scale Phylogenetic Function Annotation of Protein Families

SIFTER 2.1.1

:: DESCRIPTION

SIFTER (Statistical Inference of Function Through Evolutionary Relationships) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. SIFTER allows annotations to be made on a genomic scale.

::DEVELOPER

SIFTER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

SIFTER

:: MORE INFORMATION

Citation:

B.E. Engelhardt, M.I. Jordan, J.R. Srouji, and S.E. Brenner (2010).
Genome-scale phylogenetic function annotation of large and diverse protein families
Genome Res. 2011 July 22, 2011, doi:10.1101/gr.104687.109