Computational Biophysics and Bioinformatics

Downlodable File

1. Understanding the role of electrostatics in ion binding [Download]
2. Lysine-specific demethylase 5C (KDM5C) Homology Model [Download]
3. Representative structure of cluster regarding MTBD-MT project [Download]
4. Movies showing E-Hooks dynamics regarding MTBD-MT project [Download]
5. DelphiForce Molecular Dynamics [Download]
6. Apolipophorin III open structures [Download]

Downlodable Scripts

1. Script to visualize the zphi output from DelPhi SURFPOT Module [Download]
2. Files for MMPBSA tutorial [Download]
3. Gaussian-based-entropy-scripts [Download]

Downlodable Data

Note: There are two set of sDB (structural database) and tDB (training database)

1. sDB and tDB from Getov et. al. 2016 [PMID:27070572] [Download]
2. sDB and tDB from Petukh et. al. 2015 [PMID:26146996], 2016 [PMID:27077847] [Download]
3. Database for SAMPDI [Download]
4. Protein pKa database [Download]
5. Dataset for SAAFEC-SEQ [Download]
6. Datasets of ddG of folding or binding for point mutants used in IJMS-2023 manuscript [Download]
7. MPAD_Cleaned dataset [Download]
8. OUD GWAS large-files [Download]

Delphi Movies

1. Monte Carlo pathway for an N-kinesin motor (PDBID: 1vfv) along the microtubule [Download]
2. Monte Carlo pathway for a C-kinesin motor (PDBID: 2h58) along the microtubule [Download]
3. Monte Carlo pathway for Cin8 motor along the microtubule [Download]
4. Monte Carlo pathway for a nanoparticle along the microtubule [Download]

Delphi Resources

1. Delphi Parameter Files [Download]
2. Delphi Examples [Download]
3. Delphi Compilation Manual [Download]
4. Delphi Manual v8.5.0 [Download]