The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
MCPB.py: A Python Based Metal Center Parameter Builder
Abstract
MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.
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Cites
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Cited by
Ning, Y., Zhou, I. Y., Roberts, J. D., Rotile, N. J., Akam, E., Barrett, S. C., Sojoodi, M., Barr, M. N., Punshon, T., Pantazopoulos, P., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abq6297 · Cited by 47
Photocobilins integrate B12 and bilin photochemistry for enzyme control
Zhang, S., Jeffreys, L. N., Poddar, H., Yu, Y., Liu, C., Patel, K., Johannissen, L. O., Zhu, L., Cliff, M. J., Yan, C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46995-1 · Cited by 13
Li, P., Soudackov, A. V., & Hammes-Schiffer, S. (2018) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.8b02945 · Cited by 12
Self-citation(2025) · doi:10.1038/s41467-025-57735-4 · Cited by 10
Metadata
- Authors
- Li, P., & Merz, K. M.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-03-23
- Volume
- 56
- Issue
- 4
- Pages
- 599-604
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2275563446
- Cited by
- 730
- References
- 34
- FWCI
- 13.24
- Type
- journal article
- Language
- en
- Open access
- closed
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