ArticleComputer physics communications2021
Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis.
Article in Computer physics communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- Epistasis plays a limited role in driving entrenchment during neutral protein evolution.Genome biology · 2026Article
- Review
- Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization.Journal of medicinal chemistry · 2026Article
- Results of a large scale study of the binding of 50 type II inhibitors to 348 kinases: The role of protein reorganization.bioRxiv : the preprint server for biology · 2026Article
- Inference and Visualization of Complex Genotype-Phenotype Maps.Molecular biology and evolution · 2026Article
- Phylogenetic corrections and higher-order sequence statistics in protein families: Potts vs multiple sequence alignment transformer machine learning models.Physical review research · 2025Article
- Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges.Biophysical journal · 2025Article
- Inference and visualization of complex genotype-phenotype maps withbioRxiv : the preprint server for biology · 2025Article
- Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.bioRxiv : the preprint server for biology · 2025Article
- Article
- Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.Nature communications · 2024Article
- Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.Research square · 2024Article
- Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.bioRxiv : the preprint server for biology · 2024Article
- Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability.The journal of physical chemistry. B · 2024Article
- In vivo functional phenotypes from a computational epistatic model of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.Science advances · 2023Article
- Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases.eLife · 2022Article
- Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.The journal of physical chemistry. B · 2022Article
- Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis.Proteins · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Inverse Ising inference is a method for inferring the coupling parameters of a Potts/Ising model based on observed site-covariation, which has found important applications in protein physics for detecting interactions between residues in protein families. We introduce Mi3-GPU ("mee-three", for
Identifiers
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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.