Two decades of Martini: Better beads, broader scope
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …
been around for nearly two decades. Originally developed for lipid‐based systems by the …
Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …
processes because proteins often function within molecular complexes rather than in …
Mapping mechanostable pulling geometries of a therapeutic anticalin/CTLA-4 protein complex
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click
chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from …
chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from …
Lactoferrin inhibition of the complex formation between ACE2 receptor and SARS CoV-2 recognition binding domain
The present investigation focuses on the analysis of the interactions among human
lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin …
lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin …
Switching Go̅-Martini for Investigating Protein Conformational Transitions and Associated Protein–Lipid Interactions
Proteins are dynamic biomolecules that can transform between different conformational
states when exerting physiological functions, which is difficult to simulate using all-atom …
states when exerting physiological functions, which is difficult to simulate using all-atom …
Martini 3 OliGo̅mers: a scalable approach for multimers and fibrils in GROMACS
K Korshunova, J Kiuru, J Liekkinen… - Journal of Chemical …, 2024 - ACS Publications
Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
Transferable and polarizable coarse grained model for proteins─ ProMPT
The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-
grained level, FG), to most biomolecular processes, remains limited because of the …
grained level, FG), to most biomolecular processes, remains limited because of the …
Computational methods and theory for ion channel research
Ion channels are fundamental biological devices that act as gates in order to ensure
selective ion transport across cellular membranes; their operation constitutes the molecular …
selective ion transport across cellular membranes; their operation constitutes the molecular …
Membrane shapers from two distinct superfamilies cooperate in the development of neuronal morphology
Membrane-shaping proteins are driving forces behind establishment of proper cell
morphology and function. Yet, their reported structural and in vitro properties are noticeably …
morphology and function. Yet, their reported structural and in vitro properties are noticeably …
Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model
The Martini coarse-grain force-field has emerged as an important framework to probe
cellular processes at experimentally relevant time-and length-scales. However, the recently …
cellular processes at experimentally relevant time-and length-scales. However, the recently …