Cover Image

Software package for simulations using the coarse-grained CALVADOS model

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	von Bülow, Sören, Yasuda, Ikki, Cao, Fan, Schulze, Thea K., Trolle, Anna Ida, Rauh, Arriën Symon, Crehuet, Ramon, Lindorff-Larsen, Kresten, Tesei, Giulio
Format:	Preprint
Published:	2025
Subjects:	Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Machine learning methods to study sequence-ensemble-function relationships in disordered proteins
by: von Bülow, Sören, et al.
Published: (2024)

A coarse‐grained model for disordered proteins under crowded conditions
by: Arriën Symon Rauh, et al.
Published: (2025)

Computational design of intrinsically disordered proteins
by: Tesei, Giulio, et al.
Published: (2025)

Integrative modelling of biomolecular dynamics
by: Gusew, Daria, et al.
Published: (2025)

Detection of residual native state entropy changes upon mutation in Fyn SH3
by: Lindorff-Larsen, Kresten, et al.
Published: (2026)

Zero-shot protein stability prediction by inverse folding models: a free energy interpretation
by: Frellsen, Jes, et al.
Published: (2025)

Training a force field for proteins and small molecules from scratch
by: Blanco-González, Alexandre, et al.
Published: (2026)

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

TDP-43 multidomains and RNA modulate interactions and viscoelasticity in biomolecular condensates
by: Matsushita, Yui, et al.
Published: (2025)

Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
by: Ghafouri, Hamidreza, et al.
Published: (2025)

A unified framework for coarse grained molecular dynamics of proteins with high-fidelity reconstruction
by: Zhu, Jinzhen
Published: (2024)

The need to implement FAIR principles in biomolecular simulations
by: Amaro, Rommie, et al.
Published: (2024)

HEroBM: a deep equivariant graph neural network for universal backmapping from coarse-grained to all-atom representations
by: Angioletti, Daniele, et al.
Published: (2024)

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields
by: Cavender, Chapin E., et al.
Published: (2023)

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

BEER: Biochemical Estimator and Explorer of Residues -- A Comprehensive Software Suite for Protein Sequence Analysis
by: Mukherjee, Saumyak
Published: (2025)

Reversible molecular simulation for training classical and machine learning force fields
by: Greener, Joe G
Published: (2024)

Platelet plug microstructure and flow modulate fibrin gelation dynamics: Insights from computational simulations
by: Cruts, Janneke M. H., et al.
Published: (2026)

Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs
by: Cao, Xin, et al.
Published: (2024)

Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
by: Piomponi, Valerio, et al.
Published: (2024)

Variant effects on protein-protein interactions: methods, models and diseases
by: Larsen-Ledet, Sven, et al.
Published: (2025)

MeTime: An R package for reproducible longitudinal metabolomics data analysis
by: Marella, Bharadwaj, et al.
Published: (2026)

Conformational landscapes in cryo-ET data based on MD simulations
by: Jonic, Slavica
Published: (2026)

Integrating experimental data with molecular simulations to investigate RNA structural dynamics
by: Bernetti, Mattia, et al.
Published: (2022)

Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited
by: Tsampazi, Vasiliki, et al.
Published: (2026)

Supervised learning of protein variant effects across large‐scale mutagenesis datasets
by: Thea K. Schulze, et al.
Published: (2026)

Monte Carlo simulation of SARS-CoV-2 radiation-induced inactivation for vaccine development
by: Francis, Ziad, et al.
Published: (2020)

A potassium ion channel simulated with a universal neural network potential
by: Duignan, Timothy T.
Published: (2024)

ApexGen: Simultaneous design of peptide binder sequence and structure for target proteins
by: Xia, Xiaoqiong, et al.
Published: (2025)

Metrology of Complexity and Implications for the Study of the Emergence of Life
by: Walker, Sara Imari
Published: (2026)

SeedProteo: Accurate De Novo All-Atom Design of Protein Binders
by: Qu, Wei, et al.
Published: (2025)

Topological Enhancement of Protein Kinetic Stability
by: Especial, João NC, et al.
Published: (2026)

An RNA condensate model for the origin of life
by: Fine, Jacob L., et al.
Published: (2024)

Predicting protein folding dynamics using sequence information
by: Galpern, Ezequiel A., et al.
Published: (2025)

TumorHoPe2: An updated database for Tumor Homing Peptides
by: Kashyap, Diksha, et al.
Published: (2025)

p2smi: A Python Toolkit for Peptide FASTA-to-SMILES Conversion and Molecular Property Analysis
by: Feller, Aaron L., et al.
Published: (2025)

A review of DNA restriction-free overlapping sequence cloning techniques for synthetic biology
by: Bomfiglio, Isabella Frighetto, et al.
Published: (2025)

Ligand Pose Generation via QUBO-Based Hotspot Sampling and Geometric Triplet Matching
by: Yang, Pei-Kun
Published: (2025)

Inferring protein folding mechanisms from natural sequence diversity
by: Galpern, Ezequiel A., et al.
Published: (2024)

Leveraging Conformational Diversity for Enhanced Structure-Based Virtual Screening: Insights from Molecular Dynamics Simulations of HIV-1 Protease-Ligand Complexes
by: Yang, Pei-Kun
Published: (2025)