Developed Software/Research Tools

 

·        PBRpredict-Suite

o   A Peptide-Binding Residue Predictor-Suite (Readme)

o   Click here for code and data

 

·        PBRpredict

o   A Peptide-Binding Residue Predictor

o   Click here for code and data

 

·         BIRpredict

o   Predicts Binding Inducing Regions of Receptor Proteins in a Complex

o   Click here for data.

 

·         PCaAnalyser:

o   A 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture (publication)

o   Click here for code and data.

 

·         DisPredict:

o   Disorder Protein Predictor. Click here for code and data.

o   Tech-report (TR-2014/1), published in PLOS One in 2015.

o   CASP11’s abstract.

 

·         DisPredict2:

o   Disorder Protein Predictor version #2, includes PSEE: Position Specific Estimated Energy.

o   Corresponding article, “Estimation of Free Energy Contribution of Protein Residues as Feature for Structure Prediction from Sequence”, is coming soon.

 

·        3DIGARS:

o   Energy Function. Click here for code and data.

o   Tech-report (TR-2014/2), Accepted in Current Bioinformatics, Bentham Journal in 2015, for publication.

o   Update version 2: 3DIGARS-2.0. Click here for code, see: publication.

o   Update version 3.0: 3DIGARS-3.0. Click here for code.

§  sDFIRE:

·         Sequence-specific statistical energy function for protein structure prediction by decoy selections (published)

·         Supplementary-material. 

·         For the software, DFIRE, dDFIRE and SPINE-X are needed (can be found here: http://sparks-lab.org/index.php/Main/Downloads).

·        REGAd3p:

o   A real value predictor of Accessible Surface Area (ASA) by Regularized Exact regression, with optimization by Genetic Algorithm and using polynomial kernel of degree 3. (Layman’s summary)

o   Click here for code and data.

o   Tech-report (TR-2015/1), see: publication.

 

·         MetaSSPred:

o   A Balanced Secondary Structure Predictor (Layman’s summary)

o   Click here for code and data.

o   Tech-report (TR-2015/2), see publication.

 

·         GAPlus:

o   An Enhanced Genetic Algorithm for Ab initio Protein Structure Prediction”, DOI: 10.1109/TEVC.2015.2505317.

o   Click here for the code.

o   How to Execute.

 

·         MH_GA:

o   “Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction”, in Computational Biology and Chemistry, Elsevier (Accepted).

o   Click for the code.

 

·         Sampling:

o   Article #1: Genetic Algorithm based Improved Sampling for Protein Structure Prediction, Accepted in International Journal of Bio-Inspired Computation, Tech-report (TR-2015/4). Click for the code.

o   Article #2: hGRGA: A Scalable Genetic Algorithm using Homologous Gene Schema Replacement, Tech-report (TR-2016/1). Click for the code.

o   Article #3: AMLGA: A Genetic Algorithm with Adaptive and Memory-Assisted Local Operators, Tech-report (TR-2016/2).

 

·         Ab initio Protein Structure Predictor

o   Version 1: Click for the code.

o   Version 2: Click for the code.

 

·        Behavior Predictor, DVB

o   A Machine Learning Approach to Determine Oyster Vessel Behavior, given tracking data. Click for code and data.

 

·         NASA’s Patent Classifier Software

 

·         DataSets

o   Angle-fluctuation datasets here.