ArticleBMC structural biology2008
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.
Article in BMC structural biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Green Synthesis of Copper Nanoparticles Using Aqueous Extract of Grevillea robusta: In Vitro Antimicrobial and In Silico Approach.Chemistry & biodiversity · 2026Article
- Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.PLoS computational biology · 2025Article
- DTBind: A Mechanism-Driven Deep Learning Framework for Accurate Prediction of Drug-Target Molecular Recognition.Research (Washington, D.C.) · 2025Article
- Article
- Protein Structure Inspired Drug Discovery.bioRxiv : the preprint server for biology · 2024Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- Chemometric Models of Differential Amino Acids at the NaMolecules (Basel, Switzerland) · 2020Article
- Electrostatic recognition in substrate binding to serine proteases.Journal of molecular recognition : JMR · 2018Article
- Precision therapeutic targeting of human cancer cell motility.Nature communications · 2018Article
- VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.PLoS computational biology · 2014Article
- Assessment of ligand binding site predictions in CASP10.Proteins · 2014Article
- Virtual high-throughput ligand screening.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Identification of distant drug off-targets by direct superposition of binding pocket surfaces.PloS one · 2013Article
- Local functional descriptors for surface comparison based binding prediction.BMC bioinformatics · 2012Article
- Modeling regionalized volumetric differences in protein-ligand binding cavities.Proteome science · 2012Article
- Structure- and sequence-based function prediction for non-homologous proteins.Journal of structural and functional genomics · 2012Article
- Speeding up the drug discovery process: structural similarity searches using molecular surfaces.EMBnet.journal · 2012Article
- Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.BMC bioinformatics · 2011Article
- Protein surface characterization using an invariant descriptor.International journal of biomedical imaging · 2011Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundProtein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role.
resultsWe describe a methodology that attempts to optimize two components, global shape and local physicochemical texture, for evaluating the similarity between a pair of surfaces. Surface shape similarity is assessed using a three-dimensional object recognition algorithm and physicochemical texture similarity is assessed through a spatial alignment of conserved residues between the surfaces. The comparisons are used in tandem to efficiently search the Global Protein Surface Survey (GPSS), a library of annotated surfaces derived from structures in the PDB, for studying evolutionary relationships and uncovering novel similarities between proteins.
conclusionWe provide an assessment of our method using library retrieval experiments for identifying functionally homologous surfaces binding different ligands, functionally diverse surfaces binding the same ligand, and binding surfaces of ubiquitous and conformationally flexible ligands. Results using surface similarity to predict function for proteins of unknown function are reported. Additionally, an automated analysis of the ATP binding surface landscape is presented to provide insight into the correlation between surface similarity and function for structures in the PDB and for the subset of protein kinases.
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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.