Symmetry-invariant quantum machine learning force fields

Authors: Isabel Nha Minh Le, Oriel Kiss, Julian Schuhmacher, Ivano Tavernelli, Francesco Tacchino

Source: New Journal of Physics, Vol 27, Iss 2, p 023015 (2025)

Subject Terms: molecular force fields, geometric quantum machine learning, equivariant quantum neural networks, Science, Physics, QC1-999

File Description: electronic resource

Relation: https://doaj.org/toc/1367-2630

Access URL: https://doaj.org/article/56fd336986464c53a6c69cea483a1a8e

Frontiers in Protein Folding and Related Areas – in Memory of Professor Sir Christopher M. Dobson (1949–2019)

Contributors: Kuwajima, Kunihiro, Okamoto, Yuko, Knowles, Tuomas, Vendruscolo, Michele

Subject Terms: 14-3-3 proteins, molecular chaperone, amyloid β, α-synuclein, NMR spectroscopy, amyloid fibril, amyloidogenesis, aggregation, adsorption, Aβ 1-40 peptide, boundary of liquid phase, self-assembly, extraction, solubilization, toxic oligomers, Parkinson’s disease, familial mutations, α-helical structure, amyloid-beta, mutants, cholesterol, simulations, X-ray crystallography, phospholipase A1, homodimer, dimerization domain, catalytic triad, plant protein, molecular dynamics simulation, replica permutation method, amyloid-β, disaggregation, β-sheet, α-helix, interface, inhibitor, polyphenol, high-temperature reversible oligomerization, amyloidogenicity, oligomeric interface residues, thermal denaturation, mutational analysis, RHIM, TRIF, necroptosis, functional amyloid, fibrils, RIPK, turbulent mixing, continuous flow, fluorescence, reaction mechanism, protein folding, protein–ligand interactions, protein design, reverse fold, minimum frustration, protein structure prediction, sequence-structure alignment, template-based modeling, conditional random fields, boosted regression trees, CASP, hydrogen/deuterium exchange, dimethylsulfoxide, nuclear magnetic resonance, chaperonin, GroEL, protease, Lon protease, proteomics, proteostasis, Hfq hexamer, mutations, unfolding intermediates, thermodynamics, amyloid, insulin B chain, nucleation, prefibrillar aggregates, protofibrils, bacterial amyloid, biofilm, curli, FapC, imperfect repeats, neurodegeneration, oligomerisation, native-like, micelle, globular protein, rigid native state, molten globule, intrinsically disordered, functional state, unfolded state, coil, post-translational modifications, membrane, chaperone, statistical mechanical model, WSME model, folding kinetics, folding intermediates, protein dynamics, amyloid fibrils, amorphous aggregation, β2-microglobulin, protein misfolding, solubility, supersaturation, ultrasonication, cryo-electron microscopy, fibril, ganglioside, cancer, prion, folding, pathway, interdiction, peptide, enhanced sampling method, molecular force fields, van der Waals interaction, CHARMM36m, NBFIX, intrinsically disordered proteins, crowding simulations, Research and information: general, Biology, life sciences

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Access URL: https://directory.doabooks.org/handle/20.500.12854/100802
https://mdpi.com/books/pdfview/book/7265

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Authors: Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita

Source: Molecules, Vol 27, Iss 17, p 5726 (2022)

Subject Terms: molecular dynamics simulation, enhanced sampling method, molecular force fields, van der Waals interaction, CHARMM36m, NBFIX, Organic chemistry, QD241-441

File Description: electronic resource

Relation: https://www.mdpi.com/1420-3049/27/17/5726; https://doaj.org/toc/1420-3049

Access URL: https://doaj.org/article/7234e11b61784adda378a30adc32cf00

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