Molecular Surface Preparation

Sphere/Site Point Calculation

Grid Preparation & Interpretation

INDOCK manipulation

Processing DOCK Output

DOCK Rescoring and Minimization Tools

File Format Interconversion

File Processing Utilities

autoMS

automatic procedure for running QCPE MS using prepared receptor PDB files and setting up for sphgen

pdrenum

a versatile residue and atom renumbering utility for PDB files

get_near_res

extract receptor atoms near to ligand atoms

invertPDB

select all atoms in one PDB file which are not in another

pdb2ms

converts PDB format files into files of the format for use with QCPE MS

reformatms

convert QCPE MS files into UCSF MS files for use with sphgen

ms2dot

convert a UCSF MS file into a SYBYL dot file

condense

generate compact UCSF MS -i files

sphgen

perform sphere generation

showsphere

convert sphgen output into a displayable form

cluster

re-cluster sphgen output

colsph

labels and colors spheres

pdbtosph

convert PDB file to sphere file format

hbdata

automate Goodford's GRID for a set of probes for site point generation

mol2sph

converts MOL2 files to sphere file format

pdrenum

a versatile residue and atom renumbering utility for PDB files

showbox

create a PDB box for containing scoring grids

rebump

recreate chemgrid bump grids with altered surface contact distances

addprh

add hydrogens to proteins

reformH

convert hydrogens in SYBYL PDB output to chemgrid-readable form

charge

compute residue composition and total charge for receptor

showesp

visualize electrostatic potential from chemgrid

showprobe

visualize interaction energy of a probe on a chemgrid grid

tonew

convert DOCK 3.0 INDOCK/DOCKOPT files to 3.5 format

formatINDOCK

neatly format INDOCK files

x2pdb

convert DOCK output into standard PDB format for visualization

sortDOCKout

sort DOCK output by various metrics

fixDOCKout

fix defects in DOCK output for multi-residue ligands

splitmol

PDB/MOL2 file splitting utility

rmsd

compute rms deviation between structures in two PDB files

dockmin_dfp, dockmin_sim

optimize force-field scores of DOCK output.

scoreopt

re-score DOCK output using a chemgrid grid

shapescore

re-score DOCK output using a distmap grid

delphiscore

re-score DOCK output using a delphi grid

oldscore

re-score DOCK output using the "old" exponential algorithm from v1.1

SYBYL ASCII (MOL2) conversion

convsyb

convert MOL2 files into various formats

mol2sdf

convert MOL2 files into MDL SDF format

mol2sph

convert MOL2 files into sphere file format

PDB file exchange

x2pdb

convert DOCK output into standard PDB format for visualization

pdb2ms

convert PDB files into QCPE MS format

pdbtosph

convert PDB files into sphere file format

pdb2syb

convert PDB files into MOL2 format

x2db3

convert extended PDB DOCK output into DOCK 3.0 database

Other format exchanges

fdat2pdb

convert CSD FDAT file into PDB format

db3todb35

convert DOCK 3.0 databases into DOCK 3.5 databases

tonew

convert DOCK 3.0 INDOCK/DOCKOPT files to 3.5 format

x2db3

convert extended PDB DOCK output into DOCK 3.0 database

reformatms

convert QCPE MS files into UCSF MS files for use with sphgen

ms2dot

convert a UCSF MS file into a SYBYL dot file

addprh

add hydrogens to PDB proteins

get_near_res

extract receptor atoms near to ligand atoms

splitmol

PDB/MOL2 file splitting utility

pdrenum

a versatile residue and atom renumbering utility for PDB files

condense

generate compact UCSF MS -i files

reformH

convert hydrogens in SYBYL PDB output to chemgrid-readable form

sortDOCKout

sort DOCK output by various metrics

fixDOCKout

fix defects in DOCK output for multi-residue ligands