Copertina

Learning conformational ensembles of proteins based on backbone geometry

Fuente: arXiv

Salvato in:

Dettagli Bibliografici
Autori principali:	Wolf, Nicolas, Seute, Leif, Viliuga, Vsevolod, Wagner, Simon, Stühmer, Jan, Gräter, Frauke
Natura:	Preprint
Pubblicazione:	2025
Soggetti:	Biomolecules Statistical Mechanics Machine Learning Computational Physics
Accesso online:	Acceder al recurso
Tags:	Aggiungi Tag Nessun Tag, puoi essere il primo ad aggiungerne!!

Documenti analoghi

Flexibility-Conditioned Protein Structure Design with Flow Matching
di: Viliuga, Vsevolod, et al.
Pubblicazione: (2025)

Generating Highly Designable Proteins with Geometric Algebra Flow Matching
di: Wagner, Simon, et al.
Pubblicazione: (2024)

Interpretable machine learning of amino acid patterns in proteins: a statistical ensemble approach
di: Braghetto, Anna, et al.
Pubblicazione: (2023)

Grappa -- A Machine Learned Molecular Mechanics Force Field
di: Seute, Leif, et al.
Pubblicazione: (2024)

Determining the optimal structural resolution of proteins through an information-theoretic analysis of their conformational ensemble
di: Mele, Margherita, et al.
Pubblicazione: (2023)

Boltzmann Machine Learning with a Parallel, Persistent Markov chain Monte Carlo method for Estimating Evolutionary Fields and Couplings from a Protein Multiple Sequence Alignment
di: Miyazawa, Sanzo
Pubblicazione: (2026)

Nonequilibrium protein complexes as molecular automata
di: Kocka, Jan, et al.
Pubblicazione: (2025)

Clustering Molecular Energy Landscapes by Adaptive Network Embedding
di: Mercurio, Paula, et al.
Pubblicazione: (2024)

Learning protein-ligand unbinding pathways via single-parameter community detection
di: Tänzel, Victor, et al.
Pubblicazione: (2024)

Constrained hidden Markov models reveal further Hsp90 protein states
di: Tancredi, Riccardo, et al.
Pubblicazione: (2024)

Polyformer: a generative framework for thermodynamic modeling of polymeric molecules
di: Valentini, Alessio, et al.
Pubblicazione: (2026)

Boltzmann machine learning and regularization methods for inferring evolutionary fields and couplings from a multiple sequence alignment
di: Miyazawa, Sanzo
Pubblicazione: (2019)

Learning Potential Energy Surfaces of Hydrogen Atom Transfer Reactions in Peptides
di: Neubert, Marlen, et al.
Pubblicazione: (2025)

Structured Random Binding: a minimal model of protein-protein interactions
di: Zou, Ling-Nan
Pubblicazione: (2025)

Enzymatic Mpemba Effect: Slowing of biochemical reactions by increasing enzyme concentration
di: Hatakeyama, Tetsuhiro S.
Pubblicazione: (2024)

ENSEMBITS: an alphabet of protein conformational ensembles
di: Shi, Kaiwen, et al.
Pubblicazione: (2026)

Mechanisms of DNA-mediated allostery
di: Segers, Midas, et al.
Pubblicazione: (2023)

ATP-Dependent Mismatch Recognition in DNA Replication Mismatch Repair
di: Zhang, Nianqin, et al.
Pubblicazione: (2022)

Diffusion of intrinsically disordered proteins within viscoelastic membraneless droplets
di: Watanabe, Fuga, et al.
Pubblicazione: (2024)

Entropic tug of war: Topological constraints spontaneously rectify the dynamics of a polymer with heterogeneous fluctuations
di: Höfler, Adam H. T. P., et al.
Pubblicazione: (2024)

Data-efficient generation of protein conformational ensembles with backbone-to-side chain transformers
di: Chennakesavalu, Shriram, et al.
Pubblicazione: (2023)

The Demon Hidden Behind Life's Ultra-Energy-Efficient Information Processing -- Demonstrated by Biological Molecular Motors
di: Yanagida, Toshio, et al.
Pubblicazione: (2025)

Target search on DNA -- effect of coiling
di: Lomholt, Michael A., et al.
Pubblicazione: (2023)

Stochastic dynamics and ribosome-RNAP interactions in Transcription-Translation Coupling
di: Li, Xiangting, et al.
Pubblicazione: (2022)

Measuring irreversibility in stochastic systems by categorizing single-molecule displacements
di: Lanza, Alvaro, et al.
Pubblicazione: (2025)

Limits on Inferring T-cell Specificity from Partial Information
di: Henderson, James, et al.
Pubblicazione: (2024)

Compression-induced continuous phase transition in the buckling of a semiflexible filament for two and three dimensions
di: Mondal, Ananya, et al.
Pubblicazione: (2022)

Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs
di: Sample, Matthew, et al.
Pubblicazione: (2023)

Scaling Laws and Paradoxical Metastable States in Nanofilament Entropic Separation
di: Vilar, Jose M. G., et al.
Pubblicazione: (2026)

Field-extension statistics of charged semiflexible polymers stretched with uniform electric fields
di: Mondal, Ananya, et al.
Pubblicazione: (2024)

Representation choice shapes the interpretation of protein conformational dynamics
di: Giottonini, Axel, et al.
Pubblicazione: (2026)

Inference-time optimization for experiment-grounded protein ensemble generation
di: Maddipatla, Advaith, et al.
Pubblicazione: (2026)

A thermodynamic metric quantitatively predicts disordered protein partitioning and multicomponent phase behavior
di: Liu, Zhuang, et al.
Pubblicazione: (2026)

Actively induced supercoiling can slow down plasmid solutions by trapping the threading entanglements
di: Staňo, Roman, et al.
Pubblicazione: (2025)

Competitive ligand binding kinetics to linear polymers
di: Villaluenga, Juan P. G., et al.
Pubblicazione: (2024)

Response of Worm-like Chains to Traveling-Wave Active Forces
di: Cecconi, Fabio, et al.
Pubblicazione: (2024)

Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+
di: Laeremans, Wout, et al.
Pubblicazione: (2024)

Statistical Mechanics of Multiplectoneme Phases in DNA
di: Segers, Midas, et al.
Pubblicazione: (2024)

Towards Parsimonious Generative Modeling of RNA Families
di: Calvanese, Francesco, et al.
Pubblicazione: (2023)

Surface Induced Frustration of Inherent Dipolar Order in Nanoconfined Water
di: Mondal, Sayantan, et al.
Pubblicazione: (2025)