AlignNemo 1.1 – Local Network Alignment method to integrate Homology and Topology

AlignNemo 1.1

:: DESCRIPTION

AlignNemo (Aligning Network Modules), is a novel algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that related in sequence and topology. The subnetworks have a general topology and need not to correspond to specific interaction patterns thus more closely fit the models of functional complexes proposed in the literature.

::DEVELOPER

AlignNemo Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

AlignNemo

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38107. Epub 2012 Jun 12.
AlignNemo: a local network alignment method to integrate homology and topology.
Ciriello G, Mina M, Guzzi PH, Cannataro M, Guerra C.

HMMpTM – Transmembrane Protein Topology Prediction using Phosphorylation and Glycosylation Site Prediction

HMMpTM

:: DESCRIPTION

HMMpTM is a Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2014 Feb;1844(2):316-22. doi: 10.1016/j.bbapap.2013.11.001. Epub 2013 Nov 10.
HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.
Tsaousis GN, Bagos PG, Hamodrakas SJ.

TM-score 20190822 – Calculate Similarity of Topologies of two Protein Structures

TM-score 20190822

:: DESCRIPTION

TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TM-score

:: MORE INFORMATION

Citation

J. Xu, Y. Zhang,
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics, 2010 26, 889-895

SCAMPI2 – Improved Topology Predictions using the First and last Hydrophobic Helix Rule

SCAMPI2

:: DESCRIPTION

Given the amino acid sequence of a putative alpha-helical membrane protein, SCAMPI predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

SCAMPI2

:: MORE INFORMATION

Citation

Improved topology prediction using the terminal hydrophobic helices rule.
Peters C, Tsirigos KD, Shu N, Elofsson A.
Bioinformatics. 2015 Dec 7. pii: btv709.

OCTOPUS / SPOCTOPUS – Prediction of Membrane Protein Topology and Signal Peptides

OCTOPUS / SPOCTOPUS

:: DESCRIPTION

OCTOPUS is a new method for predicting transmembrane protein topology is presented and benchmarked using a dataset of 124 sequences with known structures.

SPOCTOPUS is a method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

OCTOPUS / SPOCTOPUS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1662-8. doi: 10.1093/bioinformatics/btn221. Epub 2008 May 12.
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.
Viklund H1, Elofsson A.

Bioinformatics. 2008 Dec 15;24(24):2928-9. doi: 10.1093/bioinformatics/btn550. Epub 2008 Oct 22.
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.
Viklund H1, Bernsel A, Skwark M, Elofsson A.

BOCTOPUS 2.0 – Topology Predictor for Beta-barrel Membrane Proteins

BOCTOPUS 2.0

:: DESCRIPTION

BOCTOPUS allows for requests of up to 1 protein sequence at a time for better predictive performance.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows
cmake.

:: DOWNLOAD

BOCTOPUS

:: MORE INFORMATION

Citation

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A.
Bioinformatics. 2016 Jan 21. pii: btw025.

Bioinformatics. 2012 Feb 15;28(4):516-22. doi: 10.1093/bioinformatics/btr710. Epub 2012 Jan 13.
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.
Hayat S1, Elofsson A.

TopoGSA – Network Topological Gene Set Analysis

TopoGSA

:: DESCRIPTION

TopoGSA (Topology-based Gene Set Analysis) computes and visualise the topological properties of a set of genes/proteins mapped onto a molecular interaction network. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, are computed and compared against those of known cellular pathways and processes (KEGG, BioCarta, GO, etc.).

::DEVELOPER

TopoGSA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 May 1;26(9):1271-2. doi: 10.1093/bioinformatics/btq131. Epub 2010 Mar 24.
TopoGSA: network topological gene set analysis.
Glaab E, Baudot A, Krasnogor N, Valencia A.

ProtOn 1603061903 – Description of Protein 3D structure in terms of Architecture, Topology and Motifs

ProtOn 1603061903

:: DESCRIPTION

ProtOn (Proteins Online): 1) draws β-sheet maps, 2) detects architectures of all-β and α/β-classes and 3) detects structural motifs containing β-strands

::DEVELOPER

Evgeniy Aksianov (evaksianov@gmail.com)

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/Linux

:: DOWNLOAD

ProtOn

:: MORE INFORMATION

TORQUE – Topology-Free Querying of Protein Interaction Networks

TORQUE

:: DESCRIPTION

TORQUE is a tool for cross-species querying of protein-protein interaction networks. Given a complex (set of proteins) for a query species, Torque seeks a matching set of proteins of a target species that are sequence-similar to the query proteins and span a connected region of the target network.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

TORQUE: topology-free querying of protein interaction networks.
Bruckner S, Hüffner F, Karp RM, Shamir R, Sharan R.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W106-8. doi: 10.1093/nar/gkp474.

STELLS2 – Inferring Species Tree from Gene Tree Topologies

STELLS2

:: DESCRIPTION

STELLS2 is a program for finding the maximum likelihood estimate of the species tree for the given gene trees, which undergo incomplete lineage sorting.

::DEVELOPER

Yufeng Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

STELLS

:: MORE INFORMATION

Citation:

Wu Y.
A Coalescent-based Method for Population Tree Inference with Haplotypes.
Bioinformatics. 2014 Oct 24. pii: btu710.

Yufeng Wu
“Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood”
Evolution, v. 66 (3), p. 763-775, 2012