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.

PhyLAT – Next-generation Sequence Similarity Search Tool

PhyLAT

:: DESCRIPTION

PhyLAT is the phylogenetic local alignment tool to compute local alignments of a query sequence against a fixed multiple-genome alignment of closely related species.

::DEVELOPER

Hongtao Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PhyLAT

:: MORE INFORMATION

Citation

H.Sun and J.Buhler,
PhyLAT – A Phylogenetic Local Alignment Tool,
Oxford Bioinformatics, 2012 (IF: 4.926)

Omokage search – Shape Similarity Search of Macromolecules

Omokage search

:: DESCRIPTION

Omokage search” is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.

::DEVELOPER

Omokage search team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Suzuki H, Kawabata T, Nakamura H.
Bioinformatics. 2015 Oct 27. pii: btv614.

IsoMIF 20150311 / IsoMIF Finder – Detection of Molecular Interaction Field Similarities

IsoMIF 20150311 / IsoMIF Finder

:: DESCRIPTION

IsoMIF identifies binding site molecular interaction field similarities between proteins. The IsoMIF Finder Interface allows you to identify binding site molecular interaction field (MIF) similarities between a query structure and a database of pre-calculated MIFs or you own custom PDB entries.

IsoMIF Finder is an online server for the identification of molecular interaction field (MIF) similarities.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IsoMIF

:: MORE INFORMATION

Citation

J Chem Inf Model. 2015 Jul 17.
Detection of Binding Site Molecular Interaction Field Similarities.
Chartier M, Najmanovich R

IsoMIF Finder: Online Detection of Binding Site Molecular Interaction Field Similarities.
Chartier M, Adriansen E, Najmanovich R.
Bioinformatics. 2015 Oct 25. pii: btv616.

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.