ArticlePloS one2020
Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Contact-Network Phenotyping of the CDK Family Reveals Selective Distal C-Lobe Contact Redistribution by Modern CDK5 Inhibitors and a Quantitative Selectivity Landscape against CDK2 and CDK1.Journal of chemical information and modeling · 2026Article
- ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models.Structural dynamics (Melville, N.Y.) · 2024Article
- Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach.Scientific reports · 2024Article
- Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction.Journal of chemical information and modeling · 2024Article
- Article
- Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae.PloS one · 2024Article
- Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions.International journal of molecular sciences · 2023Article
- Article
- Immunoinformatics Approach to Design Novel Subunit Vaccine against the Epstein-Barr Virus.Microbiology spectrum · 2022Article
- Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction.Journal of molecular biology · 2021Review
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Authors and funding
5 authors.
Funding
Abstract
Protein structures, usually visualized in various highly idealized forms focusing on the three-dimensional arrangements of secondary structure elements, can also be described as lists of interacting residues or atoms and visualized as two-dimensional distance or contact maps. We show that contact maps provide an ideal tool to describe and analyze differences between structures of proteins in different conformations. Expanding functionality of the PDBFlex server and database developed previously in our group, we describe how analysis of difference contact maps (DCMs) can be used to identify critical interactions stabilizing alternative protein conformations, recognize residues and positions controlling protein functions and build hypotheses as to molecular mechanisms of disease mutations.
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