Tag: Proteins

ASSP 1.0 – Analysis of Secondary Structure Elements in Proteins

ASSP 1.0

:: DESCRIPTION

ASSP is a Java application for analysis of secondary structure of three-dimensional protein models. It is based on the algorithm used in DSSP (Kabsch & Sander, 1983). A user-supplied structure in form of a PDB file will be analysed for H-bonding and geometric parameters to deliver a secondary structure assignment.

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 ASSP

:: MORE INFORMATION

Citation

Wang, C.K., Hofmann, A. (2014)
An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements.
3Biotech 5, 87-92.

STRIDE – Secondary Structure Assignment from known Atomic Coordinates of Proteins

STRIDE

:: DESCRIPTION

STRIDE conduct the secondary structure assignment from atomic resolution protein structures.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 STRIDE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W500-2.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.
Heinig M1, Frishman D.

HOODS – Finding Context-specific Neighborhoods of Proteins, Chemicals and Diseases

HOODS

:: DESCRIPTION

HOODS is a simple algorithm which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context.

::DEVELOPER

HOODS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 HOODS

:: MORE INFORMATION

Citation

HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases.
Palleja A, Jensen LJ.
PeerJ. 2015 Jun 30;3:e1057. doi: 10.7717/peerj.1057.

GraphPAC 1.34.0 – Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach

GraphPAC 1.34.0

:: DESCRIPTION

GraphPAC is a bioconductor R package for identifying mutational clusters of amino acids in a protein while utilizing the protein tertiary structure via a graph theoretical model.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GraphPAC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Mar 26;15(1):86. [Epub ahead of print]
A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations.
Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H.

PyInteraph 1.0 – Analysis of Interaction Networks in Structural Ensembles of Proteins

PyInteraph 1.0

:: DESCRIPTION

The PyInteraph software suite is a package designed to analyze intra- or inter-molecular interactions in structural ensembles derived both from molecular simulations or experiments (i.e. NMR-based structural ensembles)

::DEVELOPER

PyInteraph team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PyInteraph

 :: MORE INFORMATION

Citation

J Chem Inf Model. 2014 Apr 17. [Epub ahead of print]
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins.
Tiberti M1, Invernizzi G, Lambrughi M, Inbar Y, Schreiber G, Papaleo E.

Distill 2.0 – Prediction of Structural Features of Proteins

Distill 2.0

:: DESCRIPTION

Distill is a suite of public servers for the prediction of structural features of proteins. The servers can be accessed all from a single interface which also allows the submission of multiple queries.

::DEVELOPER

Gianluca Pollastri group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 15;27(20):2812-9. doi: 10.1093/bioinformatics/btr494. Epub 2011 Aug 27.
SCLpred: protein subcellular localization prediction by N-to-1 neural networks.
Mooney C1, Wang YH, Pollastri G.

Amino Acids. 2013 Aug;45(2):291-9. doi: 10.1007/s00726-013-1491-3. Epub 2013 Apr 9.
SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor.
Mooney C1, Cessieux A, Shields DC, Pollastri G.

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins.
Baú D, Martin AJ, Mooney C, Vullo A, Walsh I, Pollastri G.
BMC Bioinformatics. 2006 Sep 5;7:402.

BIS – Analysis of the Coevolution of Amino-acid Fragments in Proteins

BIS

:: DESCRIPTION

BIS (Blocks In Sequences)is a tool for the analysis of the coevolution of amino-acid fragments in proteins, and for the identification of their networks

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • Java
  • PhyML

:: DOWNLOAD

 BIS

:: MORE INFORMATION

Citation

L.Dib, A.Carbone,
Protein fragments: functional and structural roles of their coevolution networks,
PLoS ONE, 7(11): e48124, 2012.

FIRE-pro 1.1 – Motif Discovery and Characterization program in Proteins based on Mutual Information

FIRE-pro 1.1

:: DESCRIPTION

FIRE-pro (Finding Informative Regulatory Elements in proteins) is a motif discovery and characterization program for proteins based on mutual information

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Perl

:: DOWNLOAD

 FIRE-pro

:: MORE INFORMATION

Citation:

PLoS One. 2010 Dec 29;5(12):e14444. doi: 10.1371/journal.pone.0014444.
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.
Lieber DS, Elemento O, Tavazoie S.

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

CPred – Predicting Viable Circular Permutations in Proteins

CPred

:: DESCRIPTION

CPred (Circular Permutation site predictor) is a web server for predicting viable circular permutations in proteins.

::DEVELOPER

CPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W232-7. doi: 10.1093/nar/gks529. Epub 2012 Jun 11.
CPred: a web server for predicting viable circular permutations in proteins.
Lo WC1, Wang LF, Liu YY, Dai T, Hwang JK, Lyu PC.