Lab Software Description and Downloads

  • Dockeye: Software for interactive ligand-protein docking. 
  • Qnifft: Software for macromolecular electrostatics.  Supported in part by NSF grant  MCB02-35440
  • Bqequil_pdb: Software for partial charge assignment.  Supported in part by NSF grant  MCB02-35440 Yang Q, Sharp KA. Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization. J Chem Theory Comp 2006;2:1152 - 1167
  • Travel Depth: Software for determining the depth of every part of a molecular surface.  Supported in part by NSF grant  MCB02-35440 Coleman, R. G.; Sharp, K. A. J. Mol. Biol 2006.
  • Travel Distance Code 2.0: Contains Travel Depth, Travel Out and CHUNNEL algorithms .  Supported in part by NSF grant  MCB02-35440, NIH grant GM48130, Structural Biology Training Grant GM008275 and Computational Genomics Training Grant T32HG000046 Coleman, R.G.; Sharp, K.A. Biophys J 2009.
  • Travel Distance Code 3.0: Contains Travel Depth, CHUNNEL, CLIPPERS, Burial Depth.  Supported in part by NSF grant  MCB02-35440, NIH grant GM48130, Structural Biology Training Grant GM008275 and Computational Genomics Training Grant T32HG000046 Coleman, R.G.; Sharp, K.A. Proteins: Structure, Function and Bioinformatics 2009 & Coleman & Sharp, J Chem Inf Model 2010.
  • Surfmap: Software for mapping protein surfaces to a sphere.  Supported in part by NSF grant  MCB02-35440 Rahi SJ, Sharp KA. Mapping complication surfaces to a sphere. International Journal of Computational Geometry and Applications 2006
  • Surfcv: Software for calculating solvent accessible area of molecules
  • K A Sharp; A Nicholls; B Honig. DelPhi: A Macromolecular Electrostatics Software Package. Copyright Dept. of Biochemistry and Molecular Biophysics, Columbia University, New York; 1990.

© Kim A Sharp 2021