PCaAnalyser

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

Click here for code and data.

DisPredict

Disorder Protein Predictor. Click here for code and data.

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

DisPredict2

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

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

3DIGARS

Energy Function. Click here for code and data.

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

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

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).

REGAd3p

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)

Click here for code and data.

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

MetaSSPred

A Balanced Secondary Structure Predictor (Layman’s summary)

Click here for code and data.

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

GAPlus

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

Click here for the code.

How to Execute.

MH_GA

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

Click for the code.

Sampling

Article #1: Genetic Algorithms based Improved Sampling, Tech-report (TR-2015/4). Click for the code.

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

protCAD

As a Ph.D. student with William F. DeGrado at UPENN Dr. Summa wrote a library of object-oriented general-purpose protein modeling and analysis tools (in C++), primarily used for de novo protein design.