The DOI matches its Crossref record; 71 of the 71 references it cites were found in a registry or an index.
Computational design of Bax-inhibiting peptides
Open accessPublished version of a preprint
Abstract
Cyclic peptides targeting Bax were designed and evaluated via MD simulations. The peptides bind Bax with high affinity, potentially modulating its apoptotic function. This approach offers a foundation for peptide-based therapeutics.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 41,298
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 30,546
A smooth particle mesh Ewald method
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470117 · Cited by 22,514
LINCS: A linear constraint solver for molecular simulations
Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · Cited by 18,479
Canonical sampling through velocity rescaling
Bussi, G., Donadio, D., & Parrinello, M. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2408420 · Cited by 18,089
GROMACS: A message-passing parallel molecular dynamics implementation
Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995) · Computer Physics Communications · doi:10.1016/0010-4655(95)00042-e · Cited by 10,405
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 7,334
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130812 · Cited by 6,808
Apoptosis in the Pathogenesis and Treatment of Disease
Thompson, C. B. (1995) · Science · doi:10.1126/science.7878464 · Cited by 6,524
Research works printed but not linked: 4
- Baek, 2021, Science, 373, 871, 10.1126/science.abj8754 · DOI · Paper page
- S. A.Rettie , D.Juergens , V.Adebomi , Y. F.Bueso , Q.Zhao , A. N.Leveille , A.Liu , A. K.Bera , J. A.Wilms , A.Üffing , A.Kang , E.Brackenbrough , M.Lamb , S. R.Gerben , A.Murray , P. M.Levine , M.Schneider , V.Vasireddy , S.Ovchinnikov , O. H.Weiergräber , D.Willbold , J. A.Kritzer , J. D.Mougous , D.Baker , F.DiMaio and G.Bhardwaj , biorXiv, 2024
- Torrie, 1977, J. Chem. Phys., 23, 187
- Kästner, 2011, Wiley Interdiscip. Rev.: Comput. Mol. Sci., 1, 932
Metadata
- Authors
- Vlaar, T., Mayer, B., van der Heide, L., & Ilie, I. M.
- Affiliations
- University of Amsterdam (NL)
- Corresponding author
- Ilie, Ioana M.
- Venue
- Materials Advances
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2025
- Volume
- 6
- Issue
- 7
- Pages
- 2160-2169
- ISSN
- 2633-5409 (ISSN-L)
- OpenAlex
- W4407794468
- Cited by
- 2
- References
- 71
- Citations by year
- 2026: 2
- FWCI
- 0.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Materials Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Funders
- Stiftung Synapsis - Alzheimer Forschung Schweiz AFS
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- Bax, cyclic peptides, peptide design, protein-peptide interactions, apoptosis, peptide therapeutics, molecular dynamics simulation
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- Vlaar, T., Mayer, B., van der Heide, L., & Ilie, I. M. (2025). Computational design of Bax-inhibiting peptides. Materials Advances. https://doi.org/10.1039/d4ma01142b
Data sources
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.