Riepl D, Abou-Hamdan A, Gellner J, Biner O, Sjostrand D, Hogbom M
J Am Chem Soc. 2025; 147(8):6866-6879.
PMID: 39937715
PMC: 11869295.
DOI: 10.1021/jacs.4c17055.
Klaubert T, Gellner J, Bernard C, Effert J, Lombard C, Kaila V
Nat Commun. 2025; 16(1):1348.
PMID: 39905070
PMC: 11794875.
DOI: 10.1038/s41467-025-56610-6.
Bagchi S, Perez D
Nat Commun. 2025; 16(1):912.
PMID: 39837884
PMC: 11751456.
DOI: 10.1038/s41467-025-56272-4.
Hayashi A, Takamoto S, Li J, Tsuboi Y, Okanohara D
J Chem Theory Comput. 2025; 21(3):1292-1305.
PMID: 39825795
PMC: 11824368.
DOI: 10.1021/acs.jctc.4c01397.
Li H, Ma A
Nat Commun. 2025; 16(1):786.
PMID: 39824807
PMC: 11742398.
DOI: 10.1038/s41467-025-55983-y.
Ab initio machine-learning unveils strong anharmonicity in non-Arrhenius self-diffusion of tungsten.
Zhang X, Divinski S, Grabowski B
Nat Commun. 2025; 16(1):394.
PMID: 39755670
PMC: 11700192.
DOI: 10.1038/s41467-024-55759-w.
Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space.
Liu B, Boysen J, Unarta I, Du X, Li Y, Huang X
Nat Commun. 2025; 16(1):349.
PMID: 39753544
PMC: 11699157.
DOI: 10.1038/s41467-024-55228-4.
Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.
Ghosh Moulick A, Patel R, Onyema A, Loverde S
bioRxiv. 2024; .
PMID: 39574694
PMC: 11580959.
DOI: 10.1101/2024.11.05.622089.
PlmCas12e Utilizes Glu662 to Prevent Cleavage Site Occupation by Positively Charged Residues Before Target Strand Cleavage.
Liu J, Zhu L
Molecules. 2024; 29(21).
PMID: 39519677
PMC: 11547573.
DOI: 10.3390/molecules29215036.
Expanded Functionality and Portability for the Colvars Library.
Fiorin G, Marinelli F, Forrest L, Chen H, Chipot C, Kohlmeyer A
J Phys Chem B. 2024; 128(45):11108-11123.
PMID: 39501453
PMC: 11572706.
DOI: 10.1021/acs.jpcb.4c05604.
Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String.
Jia X, Xin Z, Fu Y, Duan H
Molecules. 2024; 29(20).
PMID: 39459188
PMC: 11510520.
DOI: 10.3390/molecules29204819.
Fission of double-membrane tubes under tension.
Spencer R, Santos-Perez I, Shnyrova A, Muller M
Biophys J. 2024; 123(22):3977-3996.
PMID: 39410713
PMC: 11617631.
DOI: 10.1016/j.bpj.2024.10.009.
Generating Protein Structures for Pathway Discovery Using Deep Learning.
Georgouli K, Stephany R, Tempkin J, Santiago C, Aydin F, Heimann M
J Chem Theory Comput. 2024; 20(20):8795-8806.
PMID: 39388723
PMC: 11500303.
DOI: 10.1021/acs.jctc.4c00816.
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M
J Phys Chem B. 2024; 128(41):9976-10042.
PMID: 39303207
PMC: 11492285.
DOI: 10.1021/acs.jpcb.4c04100.
Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess.
Sun Y
J Comput Chem. 2024; 46(1):e27504.
PMID: 39291721
PMC: 11586704.
DOI: 10.1002/jcc.27504.
Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.
Niu S, Ren F
Molecules. 2024; 29(11).
PMID: 38893427
PMC: 11173574.
DOI: 10.3390/molecules29112549.
Transient pores in hemifusion diaphragms.
Spencer R, Smirnova Y, Soleimani A, Muller M
Biophys J. 2024; 123(16):2455-2475.
PMID: 38867448
PMC: 11365115.
DOI: 10.1016/j.bpj.2024.06.009.
Effective data-driven collective variables for free energy calculations from metadynamics of paths.
Mullender L, Rizzi A, Parrinello M, Carloni P, Mandelli D
PNAS Nexus. 2024; 3(4):pgae159.
PMID: 38665160
PMC: 11044970.
DOI: 10.1093/pnasnexus/pgae159.
Membrane fission via transmembrane contact.
Spencer R, Santos-Perez I, Rodriguez-Renovales I, Martinez Galvez J, Shnyrova A, Muller M
Nat Commun. 2024; 15(1):2793.
PMID: 38555357
PMC: 10981662.
DOI: 10.1038/s41467-024-47122-w.
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.
Barragan A, Ghaby K, Pond M, Roux B
J Chem Inf Model. 2024; 64(8):3488-3502.
PMID: 38546820
PMC: 11386585.
DOI: 10.1021/acs.jcim.4c00023.