PyWATER 1.0 – Find Conserved Water Molecules in Proteins by clustering

PyWATER 1.0

:: DESCRIPTION

PyWATER is a PyMOL plugin to find conserved water molecules in X-ray protein structure.

::DEVELOPER

PyWATER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOs
  • Python
  • PyMOL

:: DOWNLOAD

 PyWATER

:: MORE INFORMATION

Citation

PyWATER: A PyMOL plugin to find conserved water molecules in proteins by clustering.
Patel H, Grüning BA, Günther S, Merfort I.
Bioinformatics. 2014 Jul 1. pii: btu424

Spial – Analysis of Subtype-specific Features in multiple Sequence Alignments of Proteins

Spial

:: DESCRIPTION

Spial (Specificity in alignments) is a web-server that takes a pair of multiple sequence alignments as input and produces an output that highlights positions which are conserved in both alignments (the consensus), and positions which are specific to either alignment.

::DEVELOPER

Spial team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2906-7. doi: 10.1093/bioinformatics/btq552. Epub 2010 Sep 29.
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
Wuster A1, Venkatakrishnan AJ, Schertler GF, Babu MM.

FungiFun 2.2.8 BETA – Functional Categorization of Fungal Genes and Proteins

FungiFun 2.2.8 BETA

:: DESCRIPTION

FungiFun assigns functional annotations to fungal genes or proteins. Based on different classification methods like FunCat (Functional Catalogue), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes), FungiFun categorizes genes and proteins for fungal species on different levels and conducts an enrichment analysis.

::DEVELOPER

FungiFun team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.
Priebe S, Kreisel C, Horn F, Guthke R, Linde J.
Bioinformatics. 2014 Oct 7. pii: btu627

Fungal Genet Biol. 2011 Apr;48(4):353-8. doi: 10.1016/j.fgb.2010.11.001. Epub 2010 Nov 10.
FungiFun: a web-based application for functional categorization of fungal genes and proteins.
Priebe S1, Linde J, Albrecht D, Guthke R, Brakhage AA.

iSNO-PseAAC – Predict Cysteine S-nitrosylation sites in proteins

iSNO-PseAAC

:: DESCRIPTION

iSNO-PseAAC is a new predictor which was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP) into the general form of pseudo amino acid composition (PseAAC).

::DEVELOPER

Yan Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013;8(2):e55844. doi: 10.1371/journal.pone.0055844. Epub 2013 Feb 7.
iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.
Xu Y1, Ding J, Wu LY, Chou KC.

iSNO-AAPair – Predicting the Cysteine S-nitrosylation Sites in proteins

iSNO-AAPair

:: DESCRIPTION

iSNO-AAPair is a new predictor which was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains.

::DEVELOPER

Yan Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PeerJ. 2013 Oct 3;1:e171. doi: 10.7717/peerj.171. eCollection 2013.
iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins.
Xu Y1, Shao XJ, Wu LY, Deng NY, Chou KC.

Victor 1.0 – Virtual Construction Toolkit for Proteins

Victor 1.0

:: DESCRIPTION

The Victor library is an open-source project dedicated to providing tools for analyzing and manipulating protein structures.

::DEVELOPER

Bicomputing Group, University of Padua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Victor

:: MORE INFORMATION

Citation:

The Victor C++ Library for Protein Representation and Advanced Manipulation.
Hirsh L, Piovesan D, Giollo M, Ferrari C, Tosatto SC.
Bioinformatics. 2014 Nov 19. pii: btu773

RegStatGel 1211 – Identifying differentially Expressed Proteins based on 2D Gel Images

RegStatGel 1211

:: DESCRIPTION

RegStatGel is a proteomic software for identifying differentially expressed proteins based on 2D gel images.

::DEVELOPER

Feng Li (feng.li@fda.hhs.gov)

:: SCREENSHOTS

RegStatGel

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 RegStatGel

:: MORE INFORMATION

Citation

Bioinformation. 2011;6(10):389-90. Epub 2011 Aug 2.
RegStatGel: proteomic software for identifying differentially expressed proteins based on 2D gel images.
Li F, Seillier-Moiseiwitsch F.

HMMCAS – Identifying Cas Genes and Proteins

HMMCAS

:: DESCRIPTION

HMMCAS is a program to identify Cas proteins in archaea and bacteria proteome. You can also use this web tool to find Cas proteins in your interested proteome such as giant virus.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chai G, Yu M, Jiang L, Duan Y, Huang J.
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1313-1315. doi: 10.1109/TCBB.2017.2665542. Epub 2017 Feb 7. PMID: 28186905.

TPpred 3.0 – Detection of Mitochondrial-targeting Signals in Proteins

TPpred 3.0

:: DESCRIPTION

TPpred is a web server for MITOCHONDRIAL targeting peptides prediction in proteins. TPpred is optimized for the prediction of cleavage sites of mitochondrial targeting peptides.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython
  • EMBOSS

:: DOWNLOAD

  TPpred

:: MORE INFORMATION

Citation

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in Eukaryotic proteins.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2015 Jun 16. pii: btv367

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2014 Jun 27. pii: btu411.

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.