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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

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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]

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]

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 [Download]
 
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