ArticleProceedings of the National Academy of Sciences of the United States of America2008
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed.
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- Rigid Scaffolds Are Promising for Designing Macrocyclic Kinase Inhibitors.ACS pharmacology & translational science · 2023Article
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- A Tribute to Phil Bourne-Scientist and Human.Biomolecules · 2023Article
- End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.PLoS computational biology · 2023Article
- Databases and Tools to Investigate Protein-Metabolite Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- Exploring Ligand Binding Domain Dynamics in the NRs Superfamily.International journal of molecular sciences · 2022Article
- What Makes GPCRs from Different Families Bind to the Same Ligand?Biomolecules · 2022Article
- Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- CRNNTL: Convolutional Recurrent Neural Network and Transfer Learning for QSAR Modeling in Organic Drug and Material Discovery.Molecules (Basel, Switzerland) · 2021Article
- The role of local versus nonlocal physicochemical restraints in determining protein native structure.Current opinion in structural biology · 2021Review
- Machine learning approaches and databases for prediction of drug-target interaction: a survey paper.Briefings in bioinformatics · 2021Review
- Review
- AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters.Journal of chemical information and modeling · 2020Article
- Biological representation of chemicals using latent target interaction profile.BMC bioinformatics · 2019Article
- Binding site matching in rational drug design: algorithms and applications.Briefings in bioinformatics · 2019Review
- Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.PLoS computational biology · 2019Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
Here, a scalable, accurate, reliable, and robust protein functional site comparison algorithm is presented. The key components of the algorithm consist of a reduced representation of the protein structure and a sequence order-independent profile-profile alignment (SOIPPA). We show that SOIPPA is able to detect distant evolutionary relationships in cases where both a global sequence and structure relationship remains obscure. Results suggest evolutionary relationships across several previously evolutionary distinct protein structure superfamilies. SOIPPA, along with an increased coverage of protein fold space afforded by the structural genomics initiative, can be used to further test the notion that fold space is continuous rather than discrete.
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