Difference between revisions of "SB2012"
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| + | == SB2012 Docking Database [2012.08.09 Initial Release]== | ||
| − | + | The downloads presented here refer to the publication [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments"]. The base version of the database is presented as '''Receptors, Ligands and Spheres''', which is applicable to any docking program. The spheres and grids are meant to be used with any version of the DOCK program. SB2010 is an on-going project; more structures and related resources will be added in the future. Work on [[SB2011 testset]] release is in progress. | |
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| + | Note: The DOCK energy and bump grids provided are binary files (13GB download). These were generated on an Intel Xeon, and should work fine with DOCK 4 or greater. Some platforms (e.g. ibm aix) use a different endian ordering and would require the grids to be regenerated. The grids are provided for convenience, and can be generated independently from the receptor files. The receptor and ligand mol2 files should also be compatible with most other commercial and academic docking programs. If you would like to suggest alternative file formats (pdb,sdf etc) to facilitate use with a particular tool, please contact the authors. | ||
| + | |||
| + | == DOCK Input Files == | ||
| + | |||
| + | These are the DOCK input files used to evaluate the database. | ||
| + | |||
| + | {| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%" | ||
| + | |- style="background:lightblue" | ||
| + | ! style="width:50%" !|Resource | ||
| + | ! style="width:50%" !|Filename | ||
| + | |- | ||
| + | | Rigid (RGD) | ||
| + | || [http://george.ams.sunysb.edu/SB2010/RGD.in RGD] | ||
| + | |- | ||
| + | | Fixed Anchor (FAD) | ||
| + | || [http://george.ams.sunysb.edu/SB2010/FAD.in FAD] | ||
| + | |- | ||
| + | | Flexible Ligand (FLX) | ||
| + | || [http://george.ams.sunysb.edu/SB2010/FLX.in FLX] | ||
| + | |} | ||
| + | |||
| + | == SB2012 Ligand Flexibility Subsets - Coming Soon == | ||
| + | |||
| + | |||
| + | == SB2010 Protein Families - Coming Soon == | ||
| + | |||
| + | |||
| + | == Aligned Families - Coming Soon == | ||
| + | |||
| + | |||
| + | == Sample Docking Results - Coming Soon == | ||
| + | |||
| + | |||
| + | == Copyright == | ||
| + | |||
| + | This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useable by the docking community, both academic and commercial institutions. The manuscript for this work has been accepted and is currently in press. | ||
| + | |||
| + | == Contact Information == | ||
| + | Please contact [[Image:Sudipto.email.png]] if you face any problems. <BR> | ||
| + | Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases. | ||
Revision as of 16:31, 30 November 2012
Contents
SB2012 Docking Database [2012.08.09 Initial Release]
The downloads presented here refer to the publication "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments". The base version of the database is presented as Receptors, Ligands and Spheres, which is applicable to any docking program. The spheres and grids are meant to be used with any version of the DOCK program. SB2010 is an on-going project; more structures and related resources will be added in the future. Work on SB2011 testset release is in progress.
| Resource | Filename |
|---|---|
| Receptors, Ligands and Spheres | SB2012.08.09_rec.lig.sph.tar.gz |
| Energy and Bump Grids | 2012.08.09_grids.tar.gz |
Note: The DOCK energy and bump grids provided are binary files (13GB download). These were generated on an Intel Xeon, and should work fine with DOCK 4 or greater. Some platforms (e.g. ibm aix) use a different endian ordering and would require the grids to be regenerated. The grids are provided for convenience, and can be generated independently from the receptor files. The receptor and ligand mol2 files should also be compatible with most other commercial and academic docking programs. If you would like to suggest alternative file formats (pdb,sdf etc) to facilitate use with a particular tool, please contact the authors.
DOCK Input Files
These are the DOCK input files used to evaluate the database.
| Resource | Filename |
|---|---|
| Rigid (RGD) | RGD |
| Fixed Anchor (FAD) | FAD |
| Flexible Ligand (FLX) | FLX |
SB2012 Ligand Flexibility Subsets - Coming Soon
SB2010 Protein Families - Coming Soon
Aligned Families - Coming Soon
Sample Docking Results - Coming Soon
Copyright
This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useable by the docking community, both academic and commercial institutions. The manuscript for this work has been accepted and is currently in press.
Contact Information
Please contact 
if you face any problems.
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.
