Bioinformatics Web Services, Tools and Data Sets

Web services developed by Dr. Jianlin Cheng's group since August, 2006 - present

• DOMAC: An accurate, hybrid protein domain prediction server
• MULTICOM: An accurate mlti-template comparative modeling server for protein structure prediction
• SVMcon: Protein residue contact prediction using support vector machines
• HMMVE: A visual editor for profile hidden Markov Model

      Web services developed by Dr. Jianlin Cheng in Dr. Pierre Baldi's group from 2002 - 2006

• SSpro 4.0: Protein secondary structure predictor with homology analysis
• FOLDpro: Fold recognition and template-based 3D structure prediction
• DIpro: Disulfide bond prediction
• DOMpro: Protein domain prediction 
• BETApro: Prediction of protein beta-sheet topology
• MUpro: Amino acid mutation stability prediction
• DISpro: Protein disorder region prediction
• CMAPpro 2.0 & 3Dpro: 2D contact map and ab initio 3D protein structure prediction
• SCRATCH : Protein structure prediction suites
• SIGMOID simulation: Biological network simulation web service (collaboration with Dr. Mjolsness)
• SIGMOID database: Biological network database (collaboration with Dr. Mjolsness)

     Bioinformatics Software Tools Download

• A visual editor for profile hidden Markov Model. Download HMMVE 1.0. (2007)
• Neural networks for ordinal regression and classification (Linux version). Download NNRank 1.1  (2006)
• Protein contact map prediction using support vector machines (Linux version). Download SVMcon 1.0. (2007)
• Protein secondary structure predictor. Download SSpro 4.0
• Protein solvent accessibility predictor. Download ACCpro 4.0
• Protein disulfide bond predictor. Download DIpro 2.0
• Protein beta-sheet structure predictor. Download BETApro 1.0
• Protein disordered region predictor. Download DISpro 1.0
• Protein domain predictor. Download DOMpro 1.0
• Prediction of stability changes of single site mutations from sequences. Download MUpro 1.0
• Biological Network Simulation (collaboration with Dr. Mjolsness's group). Download SIGMOID

     Bioinformatics Data Sets

• Protein disulfide bond dataset. Download SPX
• Protein disordered region dataset. Download Disorder723
• Protein beta-sheet structure dataset. Download BetaSheet916
• Protein mutation dataset. MUpro dataset
• Protein domain dataset. DOMpro dataset
• Protein fold recognition dataset. FOLDpro dataset

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