1. Handling ligands with PRODRG
Daan van Aalten
Division of Biological Chemistry and Drug Discovery
College of Life Sciences

2. PRODRG - why?
Early 1990s - no software to generate topologies for non-macromolecular entities
Manual topology generation is time consuming and error prone (but instructive)
Small molecule coordinate generators essentially only commercially available

3. PRODRG - why?
For small molecules, we need to go from imagination/some chemical info to a correct topology and optimised coordinates in seconds
+ Topologies for SHELX, REFMAC5, CNS, O, TNT, …

4. PRODRG - why? Citrate (1AJ8) NADP+ (1DDI) Cyclohexylamine (1PPA)
(1997; 1.9 Å)
(1999; 2.5 Å)
(1991; 2.0 Å)
Diphosphate (1N5L)
Sulphate (1DW9)
Ethylene glycol (1JKV)
(2002; 2.3 Å)
(1999; 1.7 Å)
(2001; 1.4 Å)

5. PRODRG History Version 1 (1995) Version 2 (2004) Version 2.5 (2005)
Started as a DRuG PROgram in GROMOS87
Takes PDB file and generates ‘MOLDES’ (SMILES-like 1D string) and MD topologies
Version 2 (2004)
Many additional input formats
Many additional output formats, including topologies for crystallographic software
Version 2.5 (2005)
Internal all-atom representation

6. PRODRG History Details covered in two publications
Webserver (~300 runs/day) with short FAQ

7. PRODRG Guts
Essentially FORTRAN (30000 lines) with some supporting C (5000) lines
Compiles well on all major platforms
Few dependencies (GROMACS for coordinate generation)

8. DB lookups & property pred.
What is PRODRG?
Generates information about small molecules
Molecular descripton
Atomic coordinates
Chemical types
Connectivity
Bond orders / aromaticity
Hybridisation
Formal charges
Atomic charges
Force field parameters
Hydrogen atoms
Free torsions
Hydrogen bonding
Model building
& refinement
PDB file
Molfile
PRODRG
Visualisation
DB lookups & property pred.
Molecular
dynamics
Docking
& analysis
Human

9. How does PRODRG work? Fixed order of steps is bad
Input analysis is rather rude:
Deletes hydrogens
Ignores bond order information
Analysis of input
Initial data gathering
Addition of hydrogens
Atom reordering
Topology generation
Formal and partial charges
Additional molecule data
Output

10. How does PRODRG work? Most steps use ‘chemical pattern matching’
Example: hydrogen generation
Add 1+sp(x)-ncon(x) hydrogens
Add 1 hydrogen
Do nothing

11. How does PRODRG work? Currently all Hs generated by 17 ‘rules’
Chemical knowledge in data, not code
More flexible
Potentially user-configurable

12. Limitations Supported atom types limited Other chemical limitations
C,H,N,O,P,S,F,Cl,Br,I only
Other chemical limitations
No more than 4 connections/atom
Standard version limited to <=300 atoms
Ignoring hydrogens and bond types may lead to unexpected results
(Apolar hydrogens as second-class atoms)
SMILES not yet implemented (but trivial)

13. Basic usage: web server
Four easy steps:
Go to

14. Basic usage: web server
Four easy steps:
Go to
Paste input

15. Basic usage: web server
Four easy steps:
Go to
Paste input
Edit settings
Chirality restraints?
Reduced charges?
Coordinates?

16. Basic usage: web server
Four easy steps:
Go to
Paste input
Edit settings
Run it

17. Basic usage: web server
Four easy steps:
Go to
Paste input
Edit settings
Run it
Success!

18. PRODRG inputs PDB coordinates MDL molfile
MOLDES (SMILES-like 1D string)
JME editor (web server)
“TEXT” input

19. Text drawings Atoms represented by their element symbols
Connected by bonds
Single: - or |
Double: = or ”
Triple: #
Change case of symbol to invert chirality
N C-C
| " "
C-C-C C-O
| | |
C=O C=C | O
N C-C
| " "
c-C-C C-O
| | |
C=O C=C | O
L-Tyr
D-Tyr

20. PRODRG outputs
PDB (generated/minimzed) coordinates (with/out hydrogens, with proper atoms names for protein/sugars/DNA), but GIGO principle applies
Quality control on input coordinates vs topology
WHAT IF topology - accurate protein-ligand Hbonds
CNS/REFMAC/TNT/SHELX topology (including PTM amino acid building blocks)
GROMOS/GROMACS/OPLS topologies
Consistent topology from crystal -> publication

21. Helping (or kicking) PRODRG
Additional commands/hints in input file:
PATCH (hybridisation)
INSHYD and DELHYD
PATCH (chirality)
PATCH (torsions)
CPNAME

22. Hybridisation hints PATCH <atom> <number>
Useful if PDB analysis did not quite work
Allows to nudge PRODRG in right direction:
PRODRG> WARNING: multiplicity of generated molecule is not 1.
PRODRG> WARNING: bond type assignment failed at CAF . O “
C=C-C
| |
C-C=N

23. Hybridisation hints PATCH <atom> <number>
Useful if PDB analysis did not quite work
Allows to nudge PRODRG in right direction: O “
C=C-C
| |
C-C=N
PATCH NAG 21

24. Adding/removing hydrogens
INSHYD <atom>
DELHYD <atom>
Allows to override default protonation
Often not actually what you want
C-C=O | O
INSHYD OAD
PRODRG> Cannot assign type to atom ' OAD'.
ERRDRG> Error in GROMOS atom names/types.
PRODRG> Drug topology not made, sorry!

25. Adding/removing hydrogens
INSHYD <atom>
DELHYD <atom>
Allows to override default protonation
Often not actually what you want
C-C=O | O
PATCH OAD 3

26. Modifying chirality PATCH <atom> -1
Inverts stereocenter <atom>, useful for PDB input
PATCH <atom> <pattern>
N C-C
| " "
C-C-C C-O
| | |
C=O C=C | O
PATCH CA L
N C-C
| " "
C-C-C C-O
| | |
C=O C=C | O
PATCH CA D
‘Absolute’ chirality for certain classes of molecules
L-Tyr
D-Tyr

27. Adding dihedral restraints
PATCH <atom> ><pattern>
After EM pyranose rings often found in undesirable conformations
PATCH statement introduces additional dihedral restraints to fix conformation
C-C-O-C-O
| | |
O C-C-C
| | |
O O O
PATCH C1 ALPHA
PATCH C2 D
PATCH C3 L
PATCH C4 D
PATCH C5 D
PATCH C1 >4C1
-D-Glucose

28. Building PRODRG can add molecular fragments to existing molecules:
BUILD <atom> <fragment>
L-Phe
BUILD CB PHI
L-Tyr
BUILD CZ OH
L-Ala

29. Building Allows quick alterations to existing molecules
Preserves coordinates of root structure
Fragment libraries contain text drawings – easy to define:
FRAG OH
X-O
FRAG PHI
X-C-C=C
" |
C-C=C
FRAG ...

30. Building
Can also be used to generate oligopeptides and oligosaccharides, using BUILD and
START <fragment>
-D-Glc
-D-NAG
-D-Man
START bdGLC
BUILD O4 adMAN1
BUILD O0F bdNAG1
PATCH C1 >4C1
PATCH C0B >4C1
PATCH C1B >4C1

31. PRODRG IP issues
Currently PRODRG freely accessible for academics through webserver and binaries
Commercial licenses (~10) have provided useful income that contributes (but does not cover) PRODRG development / maintenance
Currently no PRODRG grant funding (previously WT senior fellowship)
Thoughts on the future:
Make PRODRG as accessible as possible
Release of source?
Keen to incorporate/integrate with CCP4 but this will require some development

32. PRODRG - what next Make PRODRG as accessible as possible
Release of source?
Keen to incorporate/integrate with CCP4 but this will require some development
Need to incorporate SMILES
Make PDB input foolproof by quality control
Move away from the united-atom-with-hydrogen-addition model
Link up with GUI - not only drawing but also “building”
Link up with coot (build-place-fit ligand at pointer)

33. Acknowledgements
Alexander Schüttelkopf
PRODRG users