ArticleJournal of chemical theory and computation2022
Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 60 citations in OpenAlex.
- Artificial intelligence and ultra-high performance computing methods and experiments for drug discovery: virtual screening, deep learning, molecular dynamics simulations, ADMET modelling, and experimental validation.Molecular biomedicine · 2026Review
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Mechanism of AF9 (MLLT3)-Partner Dissociation in Mixed-Lineage Leukemia-Rearranged Leukemia.JACS Au · 2026Article
- From structure to design: experimental and AI-driven approaches in receptor-binding protein engineering for reprogramming phage host range.Archives of microbiology · 2026Review
- Study on the effects of media-regulated ultrasonic pretreatment combined with elwectrohydrodynamic drying on the drying kinetics, active components, proteomic characteristics and volatile components of garlic.Food chemistry: X · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- Dissociation kinetics of G proteins from G protein-coupled receptors and effects of allosteric modulation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Effects of Heparin Binding and Arg596 Mutations on the Conformation of Thrombin-Antithrombin Michaelis Complex, Revealed by Enhanced Sampling Molecular Dynamics Simulations.International journal of molecular sciences · 2025Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- DeepHVI: A multimodal deep learning framework for predicting human-virus protein-protein interactions using protein language models.Biosafety and health · 2025Article
- Mechanisms of Peptide Agonist Dissociation and Deactivation of Adhesion G-Protein-Coupled Receptors.Biochemistry · 2025Article
- Learning the language of plant immunity: opportunities and challenges for AI-assisted modelling of fungal effector x host protein complexes.Computational and structural biotechnology journal · 2025Review
- Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0].Living journal of computational molecular science · 2025Article
- Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD.Communications biology · 2024Article
- Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors.bioRxiv : the preprint server for biology · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Molecular Dynamics Simulations in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.Mini reviews in medicinal chemistry · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Protein-protein interactions (PPIs) play key roles in many fundamental biological processes such as cellular signaling and immune responses. However, it has proven challenging to simulate repetitive protein association and dissociation in order to calculate binding free energies and kinetics of PPIs due to long biological timescales and complex protein dynamics. To address this challenge, we have developed a new computational approach to all-atom simulations of PPIs based on a robust Gaussian accelerated molecular dynamics (GaMD) technique. The method, termed "PPI-GaMD", selectively boosts interaction potential energy between protein partners to facilitate their slow dissociation. Meanwhile, another boost potential is applied to the remaining potential energy of the entire system to effectively model the protein's flexibility and rebinding. PPI-GaMD has been demonstrated on a model system of the ribonuclease barnase interactions with its inhibitor barstar. Six independent 2 μs PPI-GaMD simulations have captured repetitive barstar dissociation and rebinding events, which enable calculations of the protein binding thermodynamics and kinetics simultaneously. The calculated binding free energies and kinetic rate constants agree well with the experimental data. Furthermore, PPI-GaMD simulations have provided mechanistic insights into barstar binding to barnase, which involves long-range electrostatic interactions and multiple binding pathways, being consistent with previous experimental and computational findings of this model system. In summary, PPI-GaMD provides a highly efficient and easy-to-use approach for binding free energy and kinetics calculations of PPIs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.