ArticleProceedings of the National Academy of Sciences of the United States of America2005
Global mapping of the protein structure space and application in structure-based inference of protein function.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
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- Molegro Data Modeller to Estimate CDK6 Inhibition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Differential Evolution for Docking Simulations.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Targeting CDK9 with Molegro Virtual Docker.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Neural Networks with Molegro Data Modeller.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Extremely Randomized Trees to Determine Binding Affinity.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Molegro Data Modeller for Machine Learning.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Calculating Enzyme Inhibition with Random Forests.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploring the Scoring Function Space with Lasso Regression.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Large protein databases reveal structural complementarity and functional locality.Nature communications · 2025Article
- Predicting Inhibition of CDK2 with SAnDReS: The Application of Machine Learning to Navigate the Scoring Function Space.Current medicinal chemistry · 2025Review
- Protein-Ligand Docking Simulations for Drug Discovery.Current medicinal chemistry · 2025Article
- Deep generative models of protein structure uncover distant relationships across a continuous fold space.Nature communications · 2024Article
- Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.Current medicinal chemistry · 2024Review
- Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python.Molecules (Basel, Switzerland) · 2023Article
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Abstract
We have constructed a map of the "protein structure space" by using the pairwise structural similarity scores calculated for all nonredundant protein structures determined experimentally. As expected, proteins with similar structures clustered together in the map and the overall distribution of structural classes of this map followed closely that of the map of the "protein fold space" we have reported previously. Consequently, proteins sharing similar molecular functions also were found to colocalize in the protein structure space map, pointing toward a previously undescribed scheme for structure-based functional inference for remote homologues based on the proximity in the map of the protein structure space. We found that this scheme consistently outperformed other predictions made by using either the raw scores or normalized Z-scores of pairwise DALI structure alignment.
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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.