Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modeling

Autor: Fallani, Alessio, Nugmanov, Ramil, Arjona-Medina, Jose, Wegner, Jörg Kurt, Tkatchenko, Alexandre, Chernichenko, Kostiantyn

We evaluate the impact of pretraining Graph Transformer architectures on atom-level quantum-mechanical features for the modeling of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of drug-like compounds. We compare th

Externí odkaz: http://arxiv.org/abs/2410.08024

$\Delta$-Machine Learning to Elevate DFT-based Potentials and a Force Field to the CCSD(T) Level Illustrated for Ethanol

Autor: Nandi, Apurba, Pandey, Priyanka, Houston, Paul L., Qu, Chen, Yu, Qi, Conte, Riccardo, Tkatchenko, Alexandre, Bowman, Joel M.

Progress in machine learning has facilitated the development of potentials that offer both the accuracy of first-principles techniques and vast increases in the speed of evaluation. Recently,"$\Delta$-machine learning" has been used to elevate the qu

Externí odkaz: http://arxiv.org/abs/2407.20050

Quantum-informed simulations for mechanics of materials: DFTB+MBD framework

Autor: Shen, Zhaoxiang, Sosa, Raúl I., Bordas, Stéphane P. A., Tkatchenko, Alexandre, Lengiewicz, Jakub

The macroscopic behaviors of materials are determined by interactions that occur at multiple lengths and time scales. Depending on the application, describing, predicting, and understanding these behaviors require models that rely on insights from el

Externí odkaz: http://arxiv.org/abs/2404.04216

Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators

Autor: Khabibrakhmanov, Almaz, Fedorov, Dmitry V., Tkatchenko, Alexandre

Repulsive short-range and attractive long-range van der Waals (vdW) forces have an appreciable role in the behavior of extended molecular systems. When using empirical force fields - the most popular computational methods applied to such systems - vd

Externí odkaz: http://arxiv.org/abs/2309.14910

Report on the sixth blind test of organic crystal-structure prediction methods

Autor: Reilly, A.M., Cooper, R.I., Adjiman, C.S., Bhattacharya, S., Boese, D.A., Brandenburg, J.G., Bygrave, P.J., Bylsma, R., Campbell, J.E., Car, R., Case, D.H., Chadha, R., Cole, J.C., Cosburn, K., Cuppen, H.M., Curtis, F., Day, G.M., DiStasio, R.A. Jr, Dzyabchenko, A., van Eijck, B.P., Elking, D.M., van den Ende, J.A., Facelli, J.C., Ferraro, M.B., Fusti-Molnar, L., Gatsiou, C-A., Gee, T.S., de Gelder, R., Ghiringhelli, L.M., Goto, H., Grimme, S., Guo, R., Hofmann, D.W.M., Hoja, J., Hylton, R.K., Iuzzolino, L., Jankiewicz, W., de Jong, D.T., Kendrick, John, de Klerk, N.J.J., Ko, H-Y., Kuleshova, L.N., Li, X., Lohani, S., Leusen, Frank J.J., Lund, A.M., Lv, J., Ma, Y., Marom, N., Masunov, A.E., McCabe, P., McMahon, D.P., Meekes, H., Metz, M.P., Misquitta, A.J., Mohamed, S., Monserrat, B., Needs, R.J., Neumann, M.A., Nyman, J., Obata, S., Oberhofer, H., Oganov, A.R., Orendt, A.M., Pagola, G.I., Pantelides, C.C., Pickard, C.J., Podeszwa, R., Price, L.S., Price, S.L., Pulido, A., Read, M.G., Reuter, K., Schneider, E., Schober, C., Shields, G.P., Singh, P., Sugden, I.J., Szalewicz, K., Taylor, C.R., Tkatchenko, A., Tuckerman, M.E., Vacarro, F., Vasileiadis, M., Vazquez-Mayagoitia, A., Vogt, L., Wang, Y., Watson, R.E., de Wijs, G.A., Yang, J., Zhu, Q., Groom, C.R.

Yes
The sixth blind test of organic crystal-structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal, and a bulky exible

Externí odkaz: http://hdl.handle.net/10454/8580