ReviewFrontiers in molecular biosciences2021
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.
Review in Frontiers in molecular biosciences, 2021. 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, 19 citations in OpenAlex.
- Protein Structure Prediction Methods.Advances in experimental medicine and biology · 2026Review
- Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology.Scientific reports · 2025Article
- Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis.Proteins · 2025Article
- Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design.Molecular biotechnology · 2025Review
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches.International journal of molecular sciences · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Computational and Functional Insights of Protein Misfolding in Neurodegeneration.Advances in experimental medicine and biology · 2023Article
- Article
- Insights into the structure and function of the histidine kinase ComP from Bacillus amyloliquefaciens based on molecular modeling.Bioscience reports · 2022Article
- AlphaFold, Artificial Intelligence (AI), and Allostery.The journal of physical chemistry. B · 2022Review
- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- Understanding structural variability in proteins using protein structural networks.Current research in structural biology · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction. Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile. Very recently, deep neural network architectures have shown promising progress in mining the coevolutionary signal encoded in multiple sequence alignments, leading to reasonably accurate estimation of inter-residue interaction maps, which serve as a rich source of additional information for improved homology detection. Here, we summarize the latest developments in protein homology detection driven by inter-residue interaction map threading. We highlight the emerging trends in distant-homology protein threading through the alignment of predicted interaction maps at various granularities ranging from binary contact maps to finer-grained distance and orientation maps as well as their combination. We also discuss some of the current limitations and possible future avenues to further enhance the sensitivity of protein homology detection.
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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.