:: DESCRIPTION
ZincExplorer is a web server that could predict Zinc-binding sites from protein sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
piNet is a resource for interactively exploring modular network models of plant immune response.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.
::DEVELOPER
Ziding Zhang’s Lab, China Agricultural University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: 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.
:: 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
:: DOWNLOAD
:: 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.