ArticleMethods in molecular biology (Clifton, N.J.)2016
Protein Residue Contacts and Prediction Methods.
Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations.Scientific reports · 2021Pooled it
- ESMDynamic: Fast and accurate prediction of protein dynamic contact maps from single sequences.Nature communications · 2026Article
- An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase.bioRxiv : the preprint server for biology · 2026Article
- In Silico Ligand-Based Screening of PDB Database for Searching Unique Motifs Against SARS-CoV-2.Biomolecules · 2026Article
- Multimodal graph, surface, and language-based model for protein protein interaction prediction.Scientific reports · 2026Article
- Article
- SpatialPPIv2: Enhancing protein-protein interaction prediction through graph neural networks with protein language models.Computational and structural biotechnology journal · 2025Article
- SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer.Computational and structural biotechnology journal · 2024Article
- Delineation of functionally essential protein regions for 242 neurodevelopmental genes.Brain : a journal of neurology · 2023Article
- COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization.Membranes · 2021Article
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
- A systematic analysis of the beta hairpin motif in the Protein Data Bank.Protein science : a publication of the Protein Society · 2021Article
- Elements of the Endomucin Extracellular Domain Essential for VEGF-Induced VEGFR2 Activity.Cells · 2020Article
- Common activation mechanism of class A GPCRs.eLife · 2019Article
- Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals.Scientific reports · 2019Article
- MISTIC2: comprehensive server to study coevolution in protein families.Nucleic acids research · 2018Article
- A deep auto-encoder model for gene expression prediction.BMC genomics · 2017Article
- An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.Acta crystallographica. Section D, Structural biology · 2017Review
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2 authors.
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Abstract
In the field of computational structural proteomics, contact predictions have shown new prospects of solving the longstanding problem of ab initio protein structure prediction. In the last few years, application of deep learning algorithms and availability of large protein sequence databases, combined with improvement in methods that derive contacts from multiple sequence alignments, have shown a huge increase in the precision of contact prediction. In addition, these predicted contacts have also been used to build three-dimensional models from scratch.In this chapter, we briefly discuss many elements of protein residue-residue contacts and the methods available for prediction, focusing on a state-of-the-art contact prediction tool, DNcon. Illustrating with a case study, we describe how DNcon can be used to make ab initio contact predictions for a given protein sequence and discuss how the predicted contacts may be analyzed and evaluated.
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