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Some Bioinformatics and Machine Learning Software Developed in the Bioinformatics, Data Mining, and Machine Learning Laboratory (BDML) since 2006

 
  • NSF Career Project - Analysis, Construction and Visualization of 3D Genome Structure (2012 - 2017)
     
  • MULTICOM Protein Structure Prediction Toolbox (NIH NIGMS funded) (one stop for all our protein structure prediction tools)  
  • i3DRefine: protein model refinement software (the top performing CASP10 model refinement server program)  
  • PSpro: a comprehensive software for 1D and 2D protein structure feature prediction  
  • APOLLO protein model quality assessment software suite including ModelEvaluator for single model quality assessment and a pairwise model quality assessment tool. Download APOLLO and ModelEvaluator  
  • Neural networks for ordinal regression and classification. Download NNRank and NNClass 1.1
  • Protein contact map prediction using support vector machines. Download SVMcon 1.0. Ranked among the best methods in CASP7,8,9 (e.g. no. 1 automated method in CASP9).
  • Protein contact map prediction using neural networks. Download NNcon 1.0. Ranked among the best methods in CASP7, 8 and 9 (e.g. no. 1 automated method in CASP8)
  • A visual editor for profile hidden Markov model. Download HMMEditor 1.0 (Java code and binary)
  • Prediction of protein folding rate (Java binary for all platforms). Download SeqRate 1.0
  • Protein secondary structure and solvent accessibility prediction using neural networks.Download SSpro 4.1 / ACCpro 4.1  
  • Protein disordered region prediction. Download PreDisorder 1.1 Ranked among the best methods in CASP7, 8 and 9 (e.g. no. 2 automated method in CASP9)  
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    Some Bioinformatics Software Developed from 2002 to 2006

     
  • 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  

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