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Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation
Alvarez, H. A., Cousido-Siah, A., Espinosa, Y. R., Podjarny, A., Carlevaro, C. M., & Howard, E. (2023). Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation. Proteins, 91(11), 1525-1534. https://doi.org/10.1002/prot.26546
Structure-based design of inhibitors of the m<sup>6</sup>A-RNA writer enzyme METTL3
Bedi, R. K., Huang, D., Li, Y., & Caflisch, A. (2023). Structure-based design of inhibitors of the m6A-RNA writer enzyme METTL3. ACS Bio & Med Chem Au, 3(4), 359-370. https://doi.org/10.1021/acsbiomedchemau.3c00023
N‐terminal β‐strand in YAP is critical for stronger binding to scalloped relative to TEAD transcription factor
Fedir, B., Yannick, M., Marco, M., Patrizia, F., Catherine, Z., Frédéric, V., … Patrick, C. (2023). N‐terminal β‐strand in YAP is critical for stronger binding to scalloped relative to TEAD transcription factor. Protein Science, 32(1), e4545 (13 pp.). https://doi.org/10.1002/pro.4545
Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s disease drug candidate
Nemergut, M., Marques, S. M., Uhrik, L., Vanova, T., Nezvedova, M., Gadara, D. C., … Marek, M. (2023). Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s disease drug candidate. Molecular Neurodegeneration, 18(1), 38 (25 pp.). https://doi.org/10.1186/s13024-023-00620-9
Combined theoretical and experimental study of the Moiré dislocation network at the SrTiO<sub>3</sub>-(La,Sr)(Al,Ta)O<sub>3</sub> interface
Ricca, C., Skoropata, E., Rossell, M. D., Erni, R., Staub, U., & Aschauer, U. (2023). Combined theoretical and experimental study of the Moiré dislocation network at the SrTiO3-(La,Sr)(Al,Ta)O3 interface. ACS Applied Materials and Interfaces, 15(46), 53678-53687. https://doi.org/10.1021/acsami.3c10958
Structure-based design of ligands of the m<sup>6</sup>A-RNA reader YTHDC1
Li, Y., Bedi, R. K., Nai, F., von Roten, V., Dolbois, A., Zálešák, F., … Caflisch, A. (2022). Structure-based design of ligands of the m6A-RNA reader YTHDC1. European Journal of Medicinal Chemistry Reports, 5, 100057 (11 pp.). https://doi.org/10.1016/j.ejmcr.2022.100057
Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism
Dietl, A., & Barends, T. R. M. (2021). Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism. Proteins, 90(1), 73-82. https://doi.org/10.1002/prot.26187
Controlling protein crystallization by free energy guided design of interactions at crystal contacts
Hermann, J., Bischoff, D., Grob, P., Janowski, R., Hekmat, D., Niessing, D., … Weuster-Botz, D. (2021). Controlling protein crystallization by free energy guided design of interactions at crystal contacts. Crystals, 11(6), 588 (18 pp.). https://doi.org/10.3390/cryst11060588
Hitting a moving target: simulation and crystallography study of ATAD2 bromodomain blockers
Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brütsch, M., Huang, D., … Caflisch, A. (2020). Hitting a moving target: simulation and crystallography study of ATAD2 bromodomain blockers. ACS Medicinal Chemistry Letters, 11(8), 1573-1580. https://doi.org/10.1021/acsmedchemlett.0c00080
Structure and molecular recognition mechanism of IMP-13 metallo-β-lactamase
Softley, C. A., Zak, K. M., Bostock, M. J., Fino, R., Zhou, R. X., Kolonko, M., … Popowicz, G. M. (2020). Structure and molecular recognition mechanism of IMP-13 metallo-β-lactamase. Antimicrobial Agents and Chemotherapy, 64(6), e00123-20 (20 pp.). https://doi.org/10.1128/AAC.00123-20
Structure of outward-facing PglK and molecular dynamics of lipid-linked oligosaccharide recognition and translocation
Perez, C., Mehdipour, A. R., Hummer, G., & Locher, K. P. (2019). Structure of outward-facing PglK and molecular dynamics of lipid-linked oligosaccharide recognition and translocation. Structure, 27(4), 669-678.e5. https://doi.org/10.1016/j.str.2019.01.013
Structures of the heart specific SERCA2a Ca&lt;sup&gt;2+&lt;/sup&gt;-ATPase
Sitsel, A., De Raeymaecker, J., Düring Drachmann, N., Derua, R., Smaardijk, S., Lauwring Andersen, J., … Nissen, P. (2019). Structures of the heart specific SERCA2a Ca2+-ATPase. EMBO Journal, 38(5), e100020 (17 pp.). https://doi.org/10.15252/embj.2018100020
Ligand retargeting by binding site analogy
Wiedmer, L., Schärer, C., Spiliotopoulos, D., Hürzeler, M., Śledź, P., & Caflisch, A. (2019). Ligand retargeting by binding site analogy. European Journal of Medicinal Chemistry, 175, 107-113. https://doi.org/10.1016/j.ejmech.2019.04.037
An unusual intramolecular halogen bond guides conformational selection
Tesch, R., Becker, C., Müller, M. P., Beck, M. E., Quambusch, L., Getlik, M., … Rauh, D. (2018). An unusual intramolecular halogen bond guides conformational selection. Angewandte Chemie International Edition, 57(31), 9970-9975. https://doi.org/10.1002/anie.201804917
Structure-based discovery of selective BRPF1 bromodomain inhibitors
Zhu, J., Zhou, C., & Caflisch, A. (2018). Structure-based discovery of selective BRPF1 bromodomain inhibitors. European Journal of Medicinal Chemistry, 155, 337-352. https://doi.org/10.1016/j.ejmech.2018.05.037
Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI
Alba, J., Marcaida, M. J., Prieto, J., Montoya, G., Molina, R., & D’Abramo, M. (2017). Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI. Journal of Computer-Aided Molecular Design, 31(12), 1063-1072. https://doi.org/10.1007/s10822-017-0087-5
Analysis of the U L&lt;sub&gt;3&lt;/sub&gt;-edge X-ray absorption spectra in UO&lt;sub&gt;2&lt;/sub&gt; using molecular dynamics simulations
Bocharov, D., Chollet, M., Krack, M., Bertsch, J., Grolimund, D., Martin, M., … Kotomin, E. (2017). Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations. Progress in Nuclear Energy, 94, 187-193. https://doi.org/10.1016/j.pnucene.2016.07.017
Improved model of proton pump crystal structure obtained by interactive molecular dynamics flexible fitting expands the mechanistic model for proton translocation in P-type ATPases
Focht, D., Croll, T. I., Pedersen, B. P., & Nissen, P. (2017). Improved model of proton pump crystal structure obtained by interactive molecular dynamics flexible fitting expands the mechanistic model for proton translocation in P-type ATPases. Frontiers in Physiology, 8, 202 (15 pp.). https://doi.org/10.3389/fphys.2017.00202
Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations
Blaum, B. S., Frank, M., Walker, R. C., Neu, U., & Stehle, T. (2016). Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations. Glycobiology, 26(5), 532-539. https://doi.org/10.1093/glycob/cwv170
An organometallic compound which exhibits a dna topology-dependent one-stranded intercalation mode
Ma, Z., Palermo, G., Adhireksan, Z., Murray, B. S., von Erlach, T., Dyson, P. J., … Davey, C. A. (2016). An organometallic compound which exhibits a dna topology-dependent one-stranded intercalation mode. Angewandte Chemie International Edition, 55(26), 7441-7444. https://doi.org/10.1002/anie.201602145