The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
ACPYPE - AnteChamber PYthon Parser interfacE
Open accessAbstract
Background: ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. Findings: We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. Conclusions: ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.
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VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
Mobley, D. L., Chodera, J. D., & Dill, K. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2221683 · Cited by 316
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Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500020m · Cited by 4,882
Accurate calculation of the absolute free energy of binding for drug molecules
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Chemical Science · doi:10.1039/c5sc02678d · Cited by 347
Colibactin DNA-damage signature indicates mutational impact in colorectal cancer
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Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.6b11467 · Cited by 177
Martini 3 Coarse-Grained Force Field for Carbohydrates
Grünewald, F., Punt, M. H., Jefferys, E. E., Vainikka, P. A., König, M., Virtanen, V., Meyer, T. A., Pezeshkian, W., Gormley, A. J., Karonen, M., et al. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00757 · Cited by 116
Metadata
- Authors
- Sousa da Silva, A. W., & Vranken, W. F.
- Venue
- BMC Research Notes
- Published
- 2012-07-23
- Volume
- 5
- Issue
- 1
- Pages
- 367-367
- ISSN
- 1756-0500 (ISSN-L)
- OpenAlex
- W2045683699
- Cited by
- 3,134
- References
- 3
- FWCI
- 19.17
- Type
- journal article
- Language
- en
- Open access
- gold
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