ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks
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Allosteric regulation, the most direct and efficient way of regulating protein function, is induced by the binding of a ligand at one site that is topographically distinct from an orthosteric site. Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) has been developed to provide comprehensive information featuring allosteric regulation. With increasing data, fundamental questions pertaining to allostery are currently receiving more attention from the mechanism of allosteric changes in an individual protein to the entire effect of the changes in the interconnected network in the cell. Thus, the following novel features were added to this updated version: (i) structural mechanisms of more than 1600 allosteric actions were elucidated by a comparison of site structures before and after the binding of an modulator; (ii) 261 allosteric networks were identified to unveil how the allosteric action in a single protein would propagate to affect downstream proteins; (iii) two of the largest human allosteromes, protein kinases and GPCRs, were thoroughly constructed; and (iv) web interface and data organization were completely redesigned for efficient access. In addition, allosteric data have largely expanded in this update. These updates are useful for facilitating the investigation of allosteric mechanisms, dynamic networks and drug discoveries.
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Orthosteric inhibitors are designed to target PPI interfaces by identifying hot spots, while allosteric modulators induce a conformational change in the target proteins by regulating their non-interaction regions when there are no hot spots defined on PPI interfaces.
“Orthosteric inhibitors are designed to target PPI interfaces by identifying hot spots, while allosteric modulators induce a conformational change in the target proteins by regulating their non-interaction regions when there are no hot spots defined on PPI interfaces.322”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [322]
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- Authors
- Shen, Q., Wang, G., Li, S., Liu, X., Lu, S., Chen, Z., Song, K., Yan, J., Geng, L., Huang, Z., Huang, W., Chen, G., & Zhang, J.
- Affiliations
- Shanghai Jiao Tong University (CN)
- Corresponding author
- Zhang, Jian
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-09-13
- Volume
- 44
- Issue
- D1
- Pages
- D527-D535
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702938
- OpenAlex
- W2175309784
- Cited by
- 122
- References
- 69
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 6 · 2023: 6 · 2022: 9 · 2021: 15 · 2020: 9 · 2019: 21 · 2018: 14 · 2017: 20 · 2016: 14
- FWCI
- 6.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Natural Science Foundation of China (81302698, 973 Program, 81473137, 2015CB910403, 81322046)
- Shanghai Rising-Star Program (13QA1402300)
- Program for New Century Excellent Talents in University (NCET-12-0355)
- National Key Research and Development Program of China (2015CB910403)
- Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- allosteric regulation, allosteric networks, allosteric modulators, protein kinases, G protein-coupled receptors, allosteric site, drug discovery, protein-protein interaction network
- MeSH terms
- Allosteric Regulation, Humans, Protein Kinases, Proteins, Signal Transduction, Internet, Databases, Protein, Receptors, G-Protein-Coupled, Drug Discovery
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