Services

Accelrys Discovery Studio (DS) Software

Founded by the CAU 985 project of Agricultural Biology and Biotechnology Innovation Platform, we have the license for the commercial molecular modeling software - Accelrys Discovery Studio (DS). The licensed DS modules include CHARMm, Biopolymer, CDOCKER, MODELER, Ligandfit, Protein Docking, etc. Currently, the software is installed and run on an IBM workstation (Z-pro 9228). For the purpose of academic use and academic research, the software is open to all the labs at CAU. Due to limited license number, interested researchers may ask your PIs to contact us for the available computational resource.

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InterSPPI

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.

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WDRR

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. The source code of WDRR is also available at: https://github.com/grittyy/WDRR.

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DescFold: Descriptor-based Fold Recognition System

DescFold(Descriptor-based Fold Recognition System) is a web server for protein fold recognition, which can predict a protein's fold type from its amino acid sequence. The server combines six effictive descriptors : a profile-sequence-alignment-based descriptor using Psi-blast e-values and bit scores, a sequence-profile-alignment-based descriptor using Rps-blast e-values and bit scores, a descriptor based on secondary structure element alignment(SSEA), a descriptor based on the occurrence of PROSITE functional motifs, a descriptor based on profile-profile-alignment(PPA) and a descriptor based on Profile-structural-profile-alignment(PSPA).

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SPAR

SPAR is a Random Forest-based method for self-interacting protein prediction. The highlight of SPAR is that the fine-grained domain-domain interaction information is taken into account.

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CKSAAP_OGlySite predictor of mucin-type O-glycosylation sites

As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins.

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pbPUP

pbPUP (Profile-Based Pupylation Site Predictor) is a computational tool to predict pupylation sites based on protein sequence information.

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TIM-Finder: A TIM-barrel Fold Recognition System

TIM-Finder (Tim-barrel Fold Recognition System) is a computational tool to predict if a query sequence belongs to TIM-barrel protein or not. By integrating sequence evolutionary information, predicted secondary structure, and sequence motif information, TIM-Finder acquired fine performance.

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piNet

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

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SSEA-OMP

SSEA-OMP (secondary structure element alignment-based outer membrane protein discrimination system) is a web server for outer membrane protein discrimination. The JAVA source code and web server that implements the SSEA algorithm are publicly available.

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ZincExplorer

ZincExplorer is a predictor of protein zinc-binding sites.

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Type III effector predictor BEAN

BEAN is a machine learning based algorithm to predict type-III effectors in bacterial pathogens.

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CKSAAP_UbSite predictor of ubiquitination sites

CKSAAP_UbSite is a web server that could predict ubiquitination sites in proteins.

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Sequence alignment algorithms

The align.tar is a package that implements Needleman-Wunsch global alignment, Smith-Waterman local alignment and secondary structure element alignment algorithms.

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