| Title |
Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide
|
|---|---|
| Published in |
Perspectives in Drug Discovery and Design, June 2009
|
| DOI | 10.1007/s10822-009-9281-4 |
| Pubmed ID | |
| Authors |
Sameer Kawatkar, Hongming Wang, Ryszard Czerminski, Diane Joseph-McCarthy |
| Abstract |
Fragment-based drug discovery approaches allow for a greater coverage of chemical space and generally produce high efficiency ligands. As such, virtual and experimental fragment screening are increasingly being coupled in an effort to identify new leads for specific therapeutic targets. Fragment docking is employed to create target-focussed subset of compounds for testing along side generic fragment libraries. The utility of the program Glide with various scoring schemes for fragment docking is discussed. Fragment docking results for two test cases, prostaglandin D2 synthase and DNA ligase, are presented and compared to experimental screening data. Self-docking, cross-docking, and enrichment studies are performed. For the enrichment runs, experimental data exists indicating that the docking decoys in fact do not inhibit the corresponding enzyme being examined. Results indicate that even for difficult test cases fragment docking can yield enrichments significantly better than random. |
Mendeley readers
The data shown below were compiled from readership statistics for 127 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 3 | 2% |
| United Kingdom | 3 | 2% |
| India | 1 | <1% |
| Switzerland | 1 | <1% |
| Germany | 1 | <1% |
| Denmark | 1 | <1% |
| Iran, Islamic Republic of | 1 | <1% |
| Japan | 1 | <1% |
| Russia | 1 | <1% |
| Other | 0 | 0% |
| Unknown | 114 | 90% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 38 | 30% |
| Researcher | 32 | 25% |
| Student > Master | 16 | 13% |
| Other | 7 | 6% |
| Professor > Associate Professor | 6 | 5% |
| Other | 19 | 15% |
| Unknown | 9 | 7% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemistry | 47 | 37% |
| Agricultural and Biological Sciences | 29 | 23% |
| Biochemistry, Genetics and Molecular Biology | 12 | 9% |
| Medicine and Dentistry | 7 | 6% |
| Pharmacology, Toxicology and Pharmaceutical Science | 6 | 5% |
| Other | 12 | 9% |
| Unknown | 14 | 11% |
Attention Score in Context
This research output has an Altmetric Attention Score of 8. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 September 2009.
All research outputs
#4,829,384
of 25,457,297 outputs
Outputs from Perspectives in Drug Discovery and Design
#214
of 949 outputs
Outputs of similar age
#20,732
of 125,482 outputs
Outputs of similar age from Perspectives in Drug Discovery and Design
#6
of 17 outputs
Altmetric has tracked 25,457,297 research outputs across all sources so far. Compared to these this one has done well and is in the 81st percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 949 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.3. This one has done well, scoring higher than 76% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 125,482 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 83% of its contemporaries.
We're also able to compare this research output to 17 others from the same source and published within six weeks on either side of this one. This one is in the 23rd percentile – i.e., 23% of its contemporaries scored the same or lower than it.