The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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Citations
Cites
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
Fast Parallel Algorithms for Short-Range Molecular Dynamics
Plimpton, S. (1995) · Journal of Computational Physics · doi:10.1006/jcph.1995.1039 · Cited by 44,721
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249
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
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Best Practices for Scientific Computing
Wilson, G., Aruliah, D. A., Brown, C. T., Chue Hong, N. P., Davis, M., Guy, R. T., Haddock, S. H. D., Huff, K. D., Mitchell, I. M., Plumbley, M. D., et al. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001745 · Cited by 723
To milliseconds and beyond: challenges in the simulation of protein folding
Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409
Self-citationMSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
Beauchamp, K. A., Bowman, G. R., Lane, T. J., Maibaum, L., Haque, I. S., & Pande, V. S. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200463m · Cited by 372
Self-citationEMMA: A Software Package for Markov Model Building and Analysis
Senne, M., Trendelkamp-Schroer, B., Mey, A. S. J. S., Schütte, C., & Noé, F. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300274u · Cited by 148
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Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
Martin, E. W., Holehouse, A. S., Peran, I., Farag, M., Incicco, J. J., Bremer, A., Grace, C. R., Soranno, A., Pappu, R. V., & Mittag, T. (2020) · Science · doi:10.1126/science.aaw8653 · Cited by 1,147
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Predicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545
Structure and dynamics of the active human parathyroid hormone receptor-1
Zhao, L.-H., Ma, S., Sutkeviciute, I., Shen, D.-D., Zhou, X. E., de Waal, P. W., Li, C.-Y., Kang, Y., Clark, L. J., Jean-Alphonse, F. G., et al. (2019) · Science · doi:10.1126/science.aav7942 · Cited by 256
Machine-learned interatomic potentials by active learning: amorphous and liquid hafnium dioxide
Sivaraman, G., Krishnamoorthy, A. N., Baur, M., Holm, C., Stan, M., Csányi, G., Benmore, C., & Vázquez-Mayagoitia, Á. (2020) · npj Computational Materials · doi:10.1038/s41524-020-00367-7 · Cited by 194
Metadata
- Authors
- McGibbon, R. T., Beauchamp, K. A., Harrigan, M. P., Klein, C., Swails, J. M., Hernández, C. X., Schwantes, C. R., Wang, L.-P., Lane, T. J., & Pande, V. S.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2015-10
- Volume
- 109
- Issue
- 8
- Pages
- 1528-1532
- ISSN
- 0006-3495 (ISSN-L)
- OpenAlex
- W2147988069
- Cited by
- 2,373
- References
- 9
- FWCI
- 33.96
- Type
- journal article
- Language
- en
- Open access
- bronze
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
