Difference between revisions of "Rizzo Lab Downloads"
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| − | The '''Flexibility Subset Lists''' divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges. Brackets marked as 'To be released' will be made available as the relevant manuscripts are submitted. SB2010 is an on-going project; more structures and related resources will be added in the future. | + | The '''Flexibility Subset Lists''' divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges. Brackets marked as 'To be released' will be made available as the relevant manuscripts are submitted. SB2010 is an on-going project; more structures and related resources will be added in the future. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor. |
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|| [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless] [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15] [http://george.ams.sunysb.edu/SB2010/15+.txt 15+] [http://george.ams.sunysb.edu/SB2010/all.txt all] | || [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless] [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15] [http://george.ams.sunysb.edu/SB2010/15+.txt 15+] [http://george.ams.sunysb.edu/SB2010/all.txt all] | ||
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== SB2010 Protein Families [2010.05.19 Initial Release] == | == SB2010 Protein Families [2010.05.19 Initial Release] == | ||
Revision as of 16:39, 20 July 2010
Contents
SB2010 Docking Database [2010.05.19 Initial Release]
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. DOCK input files used to evaluate the database are also presented.
The Flexibility Subset Lists divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges. Brackets marked as 'To be released' will be made available as the relevant manuscripts are submitted. SB2010 is an on-going project; more structures and related resources will be added in the future. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.
| Resource | Filename |
|---|---|
| Receptors, Ligands and Spheres | SB2010.05.19_rec.lig.sph.tar.gz |
| Energy and Bump Grids | To be released |
| Alternate Ligand Charge Models | To be released |
| Aligned Protein Families | To be released |
| Flexible Docked Ensembles | To be released |
| Best Flex Docked Poses | To be released |
| Unbiased Ligand Structures | To be released |
| DOCK Sample Inputs | RGD FAD FLX |
| Flexibility Subset Lists | 7orless 8to15 15+ all |
SB2010 Protein Families [2010.05.19 Initial Release]
The 25 large protein families in the database are presented as subsets below. Another 25 smaller families (i.e less than 7 members) are also present in the database. Clash subset indicates a subset of each protein family where inter-molecular clashes exist, which could possibly be resolved with flexible receptor docking. Aligned Structures contain the receptor and ligand mol2 files aligned to the first receptor in each family.
| Protein Family | Size | Clash Subset | Aligned Structures |
|---|---|---|---|
| HIV RT | 21 | To be released | To be released |
| Factor Xa | 41 | To be released | To be released |
| Neuraminidase | 43 | To be released | To be released |
| Sialidase | 11 | To be released | To be released |
| Ribonuclease T1 | 7 | To be released | To be released |
| OMP Decarboxylase | 7 | To be released | To be released |
| Estrogen Receptor | 45 | To be released | To be released |
| T4 Lysozyme | 13 | To be released | To be released |
| Beta Trypsin | 29 | To be released | To be released |
| Streptavidin | 8 | To be released | To be released |
| Thrombin | 37 | To be released | To be released |
| Tyrosine Phosphatase | 20 | To be released | To be released |
| HMG COA Reductase | 20 | To be released | To be released |
| Ribonuclease A | 14 | To be released | To be released |
| Alpha Trypsin | 46 | To be released | To be released |
| COX | 7 | To be released | To be released |
| Acetylcholinesterase | 19 | To be released | To be released |
| HIV Protease | 60 | To be released | To be released |
| Thermolysin | 26 | To be released | To be released |
| Carboxypeptidase A | 8 | To be released | To be released |
| Matrix Metalloprotease | 14 | To be released | To be released |
| Egg Lysozyme | 14 | To be released | To be released |
| Phospholipase A2 | 15 | To be released | To be released |
| Thymidylate Synthase | 12 | To be released | To be released |
| Carbonic Anhydrase | 29 | To be released | To be released |
Copyright
This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useably by the docking community, both academic and commercial institutions. The manuscript for this work has been submitted and is currently under review.
Contact Information
Please contact 
if you face any problems.
