CCharPPI Server

Available descriptors

Residue contact/step potentials

  • CP_BFKV. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_BL. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_BT. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_GKS. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_HLPL. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MJPL. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MJ3h. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MJ2h. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MJ1. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MJ2. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MSBM. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_MS. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_Qa. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_Qm. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_Qp. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_RO. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_SKOb. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_SKOa. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_SJKG. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_TD. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_TEl. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_TEs. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_TS. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_VD. Contact potential, calculated between intermolecular residues. See Proteins 59(1):49 (2005) and BMC Bioinformatics 11:92 (2010) for details. Downloaded from http://gor.bb.iastate.edu/potential/
  • CP_SKOIP. The residue level interaction contact potential described in Biophys. J. 84(3):1895 (2003).
  • CP_TB. The residue level interaction contact potential described in Proteins 62(4):970 (2006).
  • CP_TSC. The residue level interaction two-step potential described in BMC Struct biol 10:40 (2010).
  • PROPNSTS. Amino acid propensity score, described in J. Chem. Inf. Mod. 51:370 (2011).
  • CP_DDG_U. The unweighted residue potential derived from mutation data, described in J. Chem. Theory Comput. 9(8):3715-3727 (2013).
  • CP_DDG_W. The weighted residue potential derived from mutation data, described in J. Chem. Theory Comput. 9(8):3715-3727 (2013).

Residue distance-dependent potentials

  • CP_RMFCEN1. The 6bin-HRSC centroid-centroid potential described in Proteins 70(3):950 (2008).
  • CP_RMFCEN2. The 7bin-HRSC centroid-centroid potential described in Proteins 70(3):950 (2008).
  • CP_RMFCA. The C_alpha-C_alpha potential described in Proteins 65(3):726 (2006).
  • CP_D1. A reimplementation of the DECK residue level distance-dependent potential described in BMC Bioinformatics. 2011 12:280.

Atomic contact/step potentials

  • AP_T1. The first atomic two-step potential described in BMC Struct. Biol. 10:40 (2010).
  • AP_T2. The second atomic two-step potential described in BMC Struct. Biol. 10:40 (2010).
  • AP_ACE. Atomic Contact Energies (J. Mol. Biol. 267(3):707 (1997)), as integrated in FireDock: Proteins 69(1):139 (2007).
  • AP_W1. A reimplementation of the potential reported in Proteins 2007 69(3):511-20.
  • AP_DDG_U. The unweighted atomic potential derived from mutation data, described in J. Chem. Theory Comput. 9(8):3715-3727 (2013).
  • AP_DDG_W. The weighted atomic potential derived from mutation data, described in J. Chem. Theory Comput. 9(8):3715-3727 (2013).
  • AP_DARS. The DARS potential reported in Biophys J. 2008 95(9):4217-27
  • AP_URS. The URS potential reported in Biophys J. 2008 95(9):4217-27
  • AP_MPS. The MPS potential reported in Biophys J. 2008 95(9):4217-27
  • AP_OPUS_PSP. The OPUS-PSP potential described in J. Mol. Biol. 376:288 (2008).

Atomic distance-dependent potentials

  • AP_DCOMPLEX. The DComplex potential, as described in Proteins 56:93 (2004).
  • AP_dDFIRE. Interaction energy calculated using the dDFIRE potential, as described in Proteins 72:793 (2008).
  • AP_DFIRE2. Interaction energy calculated using the DFIRE2 potential, as described in Protein Science 17:1212 (2008).
  • AP_DOPE. The DOPE statistical potential described in Protein Sci. 15(11):2507 (2006).
  • AP_DOPE_HR. The high resolution DOPE statistical potential described in Protein Sci. 15(11):2507 (2006).
  • AP_calRW. The calRW distance-dependent atomic potential described in PLoS One. 2010 5(10):e15386.
  • AP_calRWp. The calRWplus orientation-dependent atomic potential described in PLoS One. 2010 5(10):e15386.
  • AP_GOAP_ALL. The total GOAP energy, as described in Biophys J. 2011 101(8): 2043-2052.
  • AP_GOAP_DF. The DFIRE term in the GOAP energy, as described in Biophys J. 2011 101(8): 2043-2052.
  • AP_GOAP_G. The GOAP_ag term in the GOAP energy, as described in Biophys J. 2011 101(8): 2043-2052.

Statistical potential constituent terms

  • CP_ZPAIR_CB. The E_pair Z-score C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ZLOCAL_CB. The E_local Z-score C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ZS3DC_CB. The E_ZS3DC z-score C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_Z3DC_CB. The E_3DC Z-score C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_EPAIR_CB. The E_pair C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ELOCAL_CB. The E_local C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ES3DC_CB. The E_ZS3DC C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_E3DC_CB. The E_3DC C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_E3D_CB. The E_3D C_beta potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ZPAIR_MIN. The E_pair Z-score R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ZLOCAL_MIN. The E_local Z-score R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ZS3DC_MIN. The E_ZS3DC z-score R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_Z3DC_MIN. The E_3DC Z-score R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_EPAIR_MIN. The E_pair R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ELOCAL_MIN. The E_local R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_ES3DC_MIN. The E_ZS3DC R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_E3DC_MIN. The E_3DC R_min potential described in Protein Sci. 2011 20(3):529-41.
  • CP_E3D_MIN. The E_3D R_min potential described in Protein Sci. 2011 20(3):529-41.

Composite scoring functions

  • ZRANK. The ZRANK scoring function reported in Proteins. 2007 67(4):1078-86.
  • ZRANK2. The ZRANK2 scoring function reported in Proteins. 2008 72(1):270-9.
  • ROSETTADOCK. Total RosettaDock weighted energy, calculated in PyRosetta: Bioinformatics 26(5):689 (2010).
  • PYDOCK_TOT. Total pyDock energy, as described in Proteins 68:503 (2007) and Protein 69:852 (2007).
  • FIREDOCK. The total FireDock energy (default energy function): Proteins 69(1):139 (2007).
  • FIREDOCK_AB. The total FireDock energy (antibody-antigen energy function): Proteins 69(1):139 (2007).
  • FIREDOCK_EI. The total FireDock energy (enzyme-inhibitor energy function): Proteins 69(1):139 (2007).
  • AP_PISA. The PISA score described in Proteins 81(4):592 (2013).
  • CP_PIE. The PIE score described in Proteins 78:400-419 (2010).
  • SIPPER. The SIPPER potential, described in J. Chem. Inf. Mod. 51:370 (2011).

Solvation energy functions

  • LK_SOLV. The Lazaridis and Karplus effective energy function (Proteins 35(2):133 (1999)), as calculated using PyRosetta: Bioinformatics 26(5):689 (2010).
  • DESOLV. Desolvation energy, as calculated using pyDock (Proteins 68:503 (2007) and Protein 69:852 (2007)).
  • ODA. The optimal docking area (ODA) score, described in Proteins 58:134-143 (2005).
  • CG_ENV. The coarse-grain environment potential implemented in PyRosetta: Bioinformatics 26(5):689 (2010).
  • CG_BETA. The coarse-grain beta potential implemented in PyRosetta: Bioinformatics 26(5):689 (2010).

Hydrogen bonding

  • HBOND. The hydrogen bonding potential integrated in FireDock: Proteins 69(1):139 (2007).
  • HBOND2. A hydrogen bonding potential, implemented in PyRosetta: Bioinformatics 26(5):689 (2010).
  • NHB. The total number of intermolecular hydrogen bonds, calculated in PyRosetta: Bioinformatics 26(5):689 (2010).

Van der Waals and electrostatics

  • CG_VDW. The coarse-grain VDW potential implemented in PyRosetta: Bioinformatics 26(5):689 (2010).
  • VDW. Van der Waals energy, as calculated using pyDock (Proteins 68:503 (2007) and Protein 69:852 (2007)).
  • FA_ATR. Attractive van der Waals energy, as calculated using PyRosetta: Bioinformatics 26(5):689 (2010).
  • FA_REP. Repulsive van der Waals energy, as calculated using PyRosetta: Bioinformatics 26(5):689 (2010).
  • ELE. Total electrostatic energy, as calculated using PyDock (Proteins 68:503 (2007) and Protein 69:852 (2007)).
  • FA_PP. The all-atom pair potential implemented in PyRosetta: Bioinformatics 26(5):689 (2010).
  • CG_PP. The coarse-grain pair potential implemented in PyRosetta: Bioinformatics 26(5):689 (2010).

Miscellaneous

  • INSIDE. Insideness concavity, as integrated in FireDock: Proteins 69(1):139 (2007).
  • PI_PI. The pi-pi potential integrated in FireDock: Proteins 69(1):139 (2007).
  • CAT_PI. The cation-pi potential integrated in FireDock: Proteins 69(1):139 (2007).
  • ALIPH. The aliphatic potential integrated in FireDock: Proteins 69(1):139 (2007).
  • ROT_S. Change in rotational entropy upon complexation.
  • TRANS_S. Change in translational entropy upon complexation.
  • NIPacking. The interface packing score described in FEBS Lett. 584(6):1163 (2010).
  • NSC. The surface complementarity score described in FEBS Lett. 584(6):1163 (2010).
  • AA_PROP. Amino acid propensity score for complex, calculated in PyRosetta: Bioinformatics 26(5):689 (2010).
  • AP_GEOMETRIC. The unpublished geometric potential of Li, X. and Liang, J, downloaded from http://gila.bioengr.uic.edu/resources/geometric.html.
  • DDG_V. A microscopic surface energy model derived from mutation data, manuscript in preparation.