Tag: Protein Sequence

HemeBIND / HemeBIND+ – Heme Binding Residue Prediction from Protein Sequence and Structure

HemeBIND / HemeBIND+

:: DESCRIPTION

HemeBIND is an efficient algorithm for predicting heme binding residues by integrating structural and sequence information.

HemeBIND+ predicts heme-binding residues based on the hybrid machine learning (with structural and sequence features) and template-based approaches.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 May 26;12:207. doi: 10.1186/1471-2105-12-207.
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.
Liu R1, Hu J.

CAPS 2.0 – Coevolution Analysis using Protein Sequences

CAPS 2.0

:: DESCRIPTION

CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.

CAPS Online Version

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 CAPS

:: MORE INFORMATION

Citation

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.

ModView 0.903 – Visualization of Multiple Protein Sequences & Structures

ModView 0.903

:: DESCRIPTION

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plug-in , it can be embed into Web pages and controlled by JavaScript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control.

::DEVELOPER

Andrej Sali

:: SCREENSHOTS

:: REQUIREMENTS

  • Netscape 4.xx

:: DOWNLOAD

ModView

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Jan;19(1):165-6.
ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.

protr 1.6-2 / ProtrWeb – Generating Various Numerical Representation Schemes of Protein Sequence

protr 1.6-2 / ProtrWeb

:: DESCRIPTION

protr is a comprehensive R package for generating various numerical representation schemes of proteins and peptides from amino acid sequence.

ProtrWeb is an online version

::DEVELOPER

Nan Xiao

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 protr

:: MORE INFORMATION

Citation

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.
Xiao N, Cao DS, Zhu MF, Xu QS.
Bioinformatics. 2015 Jan 24. pii: btv042

LCR-eXXXplorer – Search, Visualize and Share data for low Complexity Regions in Protein sequence

LCR-eXXXplorer

:: DESCRIPTION

LCR-eXXXplorer is a web-service designed to assist biologists in displaying, searching and sharing Low Complexity Regions (LCRs) contained within protein sequences.

::DEVELOPER

LCR-eXXXplorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences.
Kirmitzoglou I, Promponas VJ.
Bioinformatics. 2015 Feb 20. pii: btv115.

RBRIdent – Identification of RNA-binding Residues in Proteins from primary Sequences

RBRIdent

:: DESCRIPTION

RBRIdent is an algorithm for improved identification of RNA-binding residues in proteins from primary sequences.

::DEVELOPER

Dr. Gong’s Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • R
  • C++ Compiler

:: DOWNLOAD

  RBRIdent

:: MORE INFORMATION

Citation

Proteins. 2015 Apr 3. doi: 10.1002/prot.24806.
RBRIdent: An algorithm for improved identification of RNA-binding residues in proteins from primary sequences.
Xiong D1, Zeng J, Gong H.

ProtDCal 4.5 – Computing Multiple Numerical Descriptors for Protein Sequences and Structures

ProtDCal 4.5

:: DESCRIPTION

ProtDCal (Protein Descriptors Calculation program) is a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors.

::DEVELOPER

ProtDCal team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ProtDCal

:: MORE INFORMATION

Citation

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.
Ruiz-Blanco YB, Paz W, Green J, Marrero-Ponce Y.
BMC Bioinformatics. 2015 May 16;16:162. doi: 10.1186/s12859-015-0586-0.

TargetFreeze – Protein Sequence-based AFP predictor

TargetFreeze

:: DESCRIPTION

TargetFreeze is a supplement method to existing AFPs (Antifreeze proteins) predictors and will have potential applications in AFPs-related biotechnology fields.

::DEVELOPER

Pattern Recognition and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Membr Biol. 2015 Jun 10.
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.
He X1, Han K, Hu J, Yan H, Yang JY, Shen HB, Yu DJ.

AlignBucket – Identify Optimized Subsets of Protein Sequences for Alignment

AlignBucket

:: DESCRIPTION

AlignBucket is a software for splitting a fasta file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.

::DEVELOPER

Giuseppe Profiti , Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++

:: DOWNLOAD

 AlignBucket

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jul 30. pii: btv451.
AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints.
Profiti G, Fariselli P, Casadio R

PSIVER – Prediction of Protein-protein Interaction Sites in Protein Sequences

PSIVER

:: DESCRIPTION

PSIVER (Protein-protein interaction SItes prediction seVER)  is a server for the prediction of protein-protein interaction sites in protein sequences.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1841-8. doi: 10.1093/bioinformatics/btq302. Epub 2010 Jun 6.
Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.
Murakami Y, Mizuguchi K.

Exit mobile version