The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Pharmit: interactive exploration of chemical space
Open accessAbstract
Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.
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Cites
Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412
The PyMOL Molecular Graphics System
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Open Babel: An open chemical toolbox
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UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
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PubChem Substance and Compound databases
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436
ChEMBL: a large-scale bioactivity database for drug discovery
Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr777 · Cited by 4,382
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300687e · Cited by 2,412
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Self-citationComparison of Shape-Matching and Docking as Virtual Screening Tools
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Cited by
Gentile, D., Patamia, V., Scala, A., Sciortino, M. T., Piperno, A., & Rescifina, A. (2020) · Marine Drugs · doi:10.3390/md18040225 · Cited by 319
Next generation 3D pharmacophore modeling
Schaller, D., Šribar, D., Noonan, T., Deng, L., Nguyen, T. N., Pach, S., Machalz, D., Bermudez, M., & Wolber, G. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1468 · Cited by 269
Gao, S., Wang, L., Bai, F., & Xu, S. (2023) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2023.108614 · Cited by 12
Metadata
- Authors
- Sunseri, J., & Koes, D. R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-04-19
- Volume
- 44
- Issue
- W1
- Pages
- W442-W448
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2336883206
- Cited by
- 420
- References
- 27
- FWCI
- 11.31
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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