ArticleImmunome research2010
T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges.
Article in Immunome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Enhancing vibriosis vaccination in fish: genetically modified Nannochloropsis sp. as an oral vaccine carrier.World journal of microbiology & biotechnology · 2026Article
- Multimodal Learning of Protein-Protein Interactions for Accurate Binding Affinity Prediction.ACS omega · 2025Article
- PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models.BMC bioinformatics · 2025Article
- Experimental Validation of MHC Class I and II Peptide-Based Potential Vaccine Candidates for Human Papilloma Virus Using Sprague-Dawly Models.Molecules (Basel, Switzerland) · 2023Article
- Predicting epitopes for vaccine development using bioinformatics tools.Therapeutic advances in vaccines and immunotherapy · 2022Review
- Machine learning methods for protein-protein binding affinity prediction in protein design.Frontiers in bioinformatics · 2022Article
- Predicting antigen specificity of single T cells based on TCR CDR3 regions.Molecular systems biology · 2020Article
- Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.Current topics in medicinal chemistry · 2018Review
- The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition.Frontiers in immunology · 2017Article
- Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.BioMed research international · 2015Review
- Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.PLoS computational biology · 2014Article
- Designing immunogenic peptides.Nature chemical biology · 2013Article
- T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics.
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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.