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Forging the Basis for Developing Protein-LigandInteraction Scoring Functions

PUBLISHED September 22, 2022 (DOI: https://doi.org/10.54985/peeref.2209p6335390)

NOT PEER REVIEWED

Authors

Zhihai Liu1 , Minyi Su1 , Li Han1 , Jie Liu1 , Qifan Yang1 , Yan Li1 , Renxiao Wang1
  1. Shanghai Institute of Organic Chemistry

Conference / event

AHeDD 2017 (8th), July 2017 (Melbourne, Australia)

Poster summary

In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parameterization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous, which do not directly reflect the genuine quality of scoring functions.

Keywords

PDBbind, Structure-based drug design, CADD, Protein-ligand interactions, Scoring functions

Research areas

Chemistry, Bioinformatics and Genomics

References

  1. Yan Li, Minyi Su, Zhihai Liu, Jie Li, Jie Liu, Li Han, Renxiao Wang *, Nature Protocols, 2018, Vol. 3(4): pp 666-680.
  2. Zhihai Liu, Minyi Su, Li Han, Jie Liu, Qifan Yang, Yan Li*, and Renxiao Wang*, Accounts of Chemical Research, 2017, 50 (2): 302-309.
  3. Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao, Wei Nie, Yuchen Liu and Renxiao Wang, Bioinformatics, 2015, 31 (3): 405-412.
  4. Li, Yan; Liu, Zhihai; Li, Jie; Han, Li; Liu, Jie; Zhao, Zhi-Xiong; Wang, Renxiao*, J. Chem. Inf. Model. 2014, 54, 1700-1716.
  5. Li, Yan; Han, Li; Liu, Zhihai; Wang, Renxiao*, J. Chem. Inf. Model. 2014, 54, 1717-1736.
  6. Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. , J. Med. Chem., 2005; 48(12); 4111-4119.
  7. Wang, R.; Fang, X.; Lu, Y.; Wang, S. , J. Med. Chem., 2004; 47(12); 2977-2980.

Funding

No data provided

Supplemental files

No data provided

Additional information

Competing interests
No competing interests were disclosed.
Data availability statement
The datasets generated during and / or analyzed during the current study are available from the corresponding author on reasonable request.
Creative Commons license
Copyright © 2022 Liu et al. This is an open access work distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Liu, Z., Su, M., Han, L., Liu, J., Yang, Q., Li, Y., Wang, R. Forging the Basis for Developing Protein-LigandInteraction Scoring Functions [not peer reviewed]. Peeref 2022 (poster).
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