ProteinModelerABC

:: DESCRIPTION

ProteinModelerABC is an evolutionary framework to estimate the best-fitting substitution model of protein evolution, among a set of complex substitution models that cannot be analyzed with traditional phylogenetic likelihood functions, with the approximate Bayesian computation (ABC) approach.

::DEVELOPER

David Ferreiro, Catarina Branco, Miguel Arenas

:: REQUIREMENTS

Linux

:: DOWNLOAD

ProteinModelerABC

:: MORE INFORMATION

Citation

Ferreiro D, Branco C, Arenas M. 2024.
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.
Bioinformatics, 40:3, btae096. https://doi.org/10.1093/bioinformatics/btae096

ProtASR 2.2 – Ancestral Sequence Reconstruction of Proteins accounting for Structural Constraints

ProtASR 2.2

:: DESCRIPTION

ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.

::DEVELOPER

Dr. Miguel Arenas

:: REQUIREMENTS

Linux

:: DOWNLOAD

ProtASR

:: MORE INFORMATION

Citation

Arenas M, Bastolla U.
ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability.
Methods Ecol Evol. 2020; 11: 248–257. https://doi.org/10.1111/2041-210X.13341

POPGENE 1.32 – Population Genetic Analysis

POPGENE 1.32

:: DESCRIPTION

POPGENE is a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. This package provides the Windows graphical user interface that makes population genetics analysis more accessible for the casual computer user and more convenient for the experienced computer user. Simple menus and dialog box selections enable you to perform complex analyses and produce scientifically sound statistics, thereby assisting you to adequately analyze population genetic structure using the target markers.

::DEVELOPER

POPGENE Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

POPGENE

:: MORE INFORMATION

GeneFinder 1.2.7 – Linkage Analysis with a Variety of Extensions

GeneFinder 1.2.7

:: DESCRIPTION

GeneFinder is a software package for linkage analysis with a variety of extensions. GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc.

::DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

GeneFinder

:: MORE INFORMATION

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

:: 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

:: 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.