ZincExplorer – Predictor of Protein Zinc-binding Sites

ZincExplorer

:: DESCRIPTION

ZincExplorer is a web server that could predict Zinc-binding sites from protein sequence.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Mol Biosyst. 2013 Sep;9(9):2213-22. doi: 10.1039/c3mb70100j.
ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.
Chen Z, Wang Y, Zhai YF, Song J, Zhang Z.

piNet – Modular Network Models of Plant Immune Reponse

piNet

:: DESCRIPTION

piNet is a resource for interactively exploring modular network models of plant immune response.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Dong X., Jiang Z., Peng Y-L., Zhang Z. (2015)
Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis.
Plant Physiol. 2015 Mar;167(3):1186-203. doi: 10.1104/pp.114.254292.

WDRR – WD40 Repeat Recognition

WDRR

:: DESCRIPTION

WDRR is a new WD40 Repeat Recognition method, which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server
  • PHP

:: DOWNLOAD

WDRR

:: MORE INFORMATION

Citation

J Theor Biol. 2016 Jun 7;398:122-9. doi: 10.1016/j.jtbi.2016.03.025.
Identification of WD40 repeats by secondary structure-aided profile-profile alignment.
Wang C, Dong X, Han L, Su XD, Zhang Z, Li J, Song J

SPAR v1.0 – Predictor for self-interacting protein from Sequence Information

SPAR v1.0

:: DESCRIPTION

SPAR (Self-interacting Protein AnalyzeR) was a predictor for self-interacting protein from sequence information. Based on comprehensive analysis of a variety of physiochemical properties on self-interacting proteins, a new encoding scheme named RSI has been designed.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SPAR

:: MORE INFORMATION

Citation

Amino Acids. 2016 Jul;48(7):1655-65. doi: 10.1007/s00726-016-2226-z.
SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information.
Liu X, Yang S, Li C, Zhang Z, Song J.

InterSPPI v1.3 – AraPathogen predicts PPIs between Arabidopsis thaliana and pathogens

InterSPPI v1.3

:: DESCRIPTION

InterSPPI is a web server that could predict protein-protein interactions (PPIs) between Arabidopsis thaliana and pathogens based on sequence and Arabidopsis thaliana intra-species PPI network (AraPPI) information.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

InterSPPI

:: MORE INFORMATION

Citation

Brief Bioinform. 2019 Jan 18;20(1):274-287. doi: 10.1093/bib/bbx123.
Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods.
Yang S, Li H, He H, Zhou Y, Zhang Z.

CKSAAP_UbSite / hCKSAAP_UbSite – A Predictor of Protein Ubiquitination sites

CKSAAP_UbSite / hCKSAAP_UbSite

:: DESCRIPTION

CKSAAP_UbSite (composition of k-spaced amino acid pairs) is a web server that could predict ubiquitination sites in proteins.

hCKSAAP_UbSite is a web server for improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

CKSAAP_UbSite / hCKSAAP_UbSite

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. doi: 10.1016/j.bbapap.2013.04.006.
hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
Chen Z1, Zhou Y, Song J, Zhang Z.

MEPI – Predict Catalytic Residues from Protein Structures

MEPI

:: DESCRIPTION

The MEPI is a web server to predict catalytic residues from protein structures, which integrates the Micro-Environment(ME) and Position Information of each residue.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(7):e41370. doi: 10.1371/journal.pone.0041370. Epub 2012 Jul 19.
Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues.
Han L1, Zhang YJ, Song J, Liu MS, Zhang Z.

MAPanalyzer – Analyzing Microtubule-associated Proteins

MAPanalyzer

:: DESCRIPTION

MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
Zhou Y, Yang S, Mao T, Zhang Z.
Database (Oxford). 2015 Nov 13;2015. pii: bav108. doi: 10.1093/database/bav108.

BEAN 2.0 – Bacteria Effector ANalyzer

BEAN 2.0

:: DESCRIPTION

BEAN is a machine learning based algorithm to predict type-III effectors in bacterial pathogens. It uses features of type-III secretion signal learned from known type-III effectors to predict query proteins as effectors or non-effectors.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BEAN

:: MORE INFORMATION

Citation

Database (Oxford). 2015 Jun 27;2015:bav064. doi: 10.1093/database/bav064.
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors.
Dong X, Lu X, Zhang Z.

PLoS One. 2013;8(2):e56632. doi: 10.1371/journal.pone.0056632.
Using weakly conserved motifs hidden in secretion signals to identify type-III effectors from bacterial pathogen genomes.
Dong X1, Zhang YJ, Zhang Z.

SSEA-OMP – Outer Membrane Protein Discrimination

SSEA-OMP

:: DESCRIPTION

SSEA-OMP (Secondary Structure Element Alignment-based Outer Membrane Protein Discrimination system) is a web server for outer membrane protein discrimination.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SSEA-OMP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Mar 17;12:76. doi: 10.1186/1471-2105-12-76.
Outer membrane proteins can be simply identified using secondary structure element alignment.
Yan RX1, Chen Z, Zhang Z.

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