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

Mash v2.2 – Fast Similarity Estimates via MinHash

Mash v2.2

:: DESCRIPTION

Mash is a software of fast genome and metagenome distance estimation using MinHash

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Mash

:: MORE INFORMATION

Citation:

Genome Biol, 17 (1), 132
Mash: Fast Genome and Metagenome Distance Estimation Using MinHash
Brian D Ondov , Todd J Treangen , Páll Melsted , Adam B Mallonee , Nicholas H Bergman , Sergey Koren , Adam M Phillippy

NaviGO – An analytic tool for Gene Ontology Visualization and Similarity

NaviGO

:: DESCRIPTION

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

EFI-EST – Generating Protein Sequence Similarity Networks

EFI-EST

:: DESCRIPTION

EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool  is available without cost for the automated generation of protein sequence similarity networks.

::DEVELOPER

EFI-EST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.
Biochim Biophys Acta. 2015 Apr 18. pii: S1570-9639(15)00112-0. doi: 10.1016/j.bbapap.2015.04.015.

Rchemcpp 2.24.0 – An R package for Computing the Similarity of Molecules

Rchemcpp 2.24.0

:: DESCRIPTION

Chemcpp is an R package that is the computation of similarities between molecules by kernel functions.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

Rchemcpp

:: MORE INFORMATION

Citation

Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map.
Klambauer G, Wischenbart M, Mahr M, Unterthiner T, Mayr A, Hochreiter S.
Bioinformatics. 2015 Oct 15;31(20):3392-4. doi: 10.1093/bioinformatics/btv373.

MCQ4Structures 1.6.1 – Computing Similarity of 3D RNA / Protein Structures

MCQ4Structures 1.6.1

:: DESCRIPTION

MCQ4Structures is a tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. Although it has been primarily designed to work with RNA structures, MCQ4Structures can be also applied to proteins (however their representation is restricted to the backbone angles).

::DEVELOPER

Tomasz Żok

:: SCREENSHOTS

MCQ4Structures

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Java

:: DOWNLOAD

 MCQ4Structures

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Oct 23;18(1):456. doi: 10.1186/s12859-017-1867-6.
LCS-TA to identify similar fragments in RNA 3D structures.
Wiedemann J, Zok T, Milostan M, Szachniuk M

PSS 20091105 – Protein Profile Similarity Screening

PSS 20091105

:: DESCRIPTION

PSS is a matlab code of computational protein profile similarity screening for quantitative mass spectrometry experiments.

::DEVELOPER

Hamprecht lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 PSS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):77-83. doi: 10.1093/bioinformatics/btp607. Epub 2009 Oct 27.
Computational protein profile similarity screening for quantitative mass spectrometry experiments.
Kirchner M1, Renard BY, Köthe U, Pappin DJ, Hamprecht FA, Steen H, Steen JA.

MeSHSim 1.4.0 – R Package for Calculating Similarity Among MEDLINE Subject Headings

MeSHSim 1.4.0

:: DESCRIPTION

MeSHSim is the most integrated R package for calculating Similarity among Medline Subject Headings.

::DEVELOPER

Lab of Data Mining and Intelligent Information Processing (DM&IIP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/ BioConductor

:: DOWNLOAD

 MeSHSim

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2015 Dec;13(6):1542002. doi: 10.1142/S0219720015420020. Epub 2015 Sep 9.
MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.
Zhou J, Shui Y, Peng S, Li X, Mamitsuka H, Zhu S.

GeneExpressionSignature 1.16.0 – Gene Expression Signature based Similarity Metric

GeneExpressionSignature 1.16.0

:: DESCRIPTION

GeneExpressionSignature gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

::DEVELOPER

Yang Cao <yiluheihei at gmail.com>, Fei Li <pittacus at gmail.com>,Lu Han <hanl8910 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 GeneExpressionSignature

:: MORE INFORMATION

Citation

OMICS. 2013 Feb;17(2):116-8. doi: 10.1089/omi.2012.0087.
GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.
Li F1, Cao Y, Han L, Cui X, Xie D, Wang S, Bo X.

OAT 0.91 – Similarity Measurement Tool for Genomes

OAT 0.91

:: DESCRIPTION

OAT (Orthologous Average Nucleotide Identity Tool) uses OrthoANI to measure overall similarity between two genome sequences.

::DEVELOPER

OAT team

:: SCREENSHOTS

OAT

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 OAT

:: MORE INFORMATION

Citation:

OrthoANI: An improved algorithm and software for calculating average nucleotide identity.
Lee I, Kim YO, Park SC, Chun J.
Int J Syst Evol Microbiol. 2015 Nov 18. doi: 10.1099/ijsem.0.000760.