ArticlePLoS computational biology2010
VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 59 citations in OpenAlex.
- CaviDB: a database of cavities and their features in the structural and conformational space of proteins.Database : the journal of biological databases and curation · 2023Article
- General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model.Molecular biology and evolution · 2022Article
- Article
- A Conical Representation of Hydrogen Bond Geometry for Quantifying Bond Interactions.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2021Article
- Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials.Algorithms for molecular biology : AMB · 2020Article
- Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants.Journal of chemical information and modeling · 2019Article
- Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia.BMC bioinformatics · 2018Article
- A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme.Science (New York, N.Y.) · 2018Article
- Exploring Protein Cavities through Rigidity Analysis.Molecules (Basel, Switzerland) · 2018Article
- Structure-guided selection of specificity determining positions in the human Kinome.BMC genomics · 2016Article
- VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.PLoS computational biology · 2014Article
- Article
- HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking.Proteome science · 2013Article
- An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.BMC structural biology · 2013Article
- Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.Nucleic acids research · 2013Article
- Modeling regionalized volumetric differences in protein-ligand binding cavities.Proteome science · 2012Article
- Article
- Speeding up the drug discovery process: structural similarity searches using molecular surfaces.EMBnet.journal · 2012Article
- Accuracy of functional surfaces on comparatively modeled protein structures.Journal of structural and functional genomics · 2011Article
- MarkUs: a server to navigate sequence-structure-function space.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP), a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dimensionally superposed volumes. We applied VASP to compute a comparative volumetric analysis of the ligand binding sites formed by members of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains and the serine proteases. Within both families, VASP isolated individual amino acids that create structural differences between ligand binding cavities that are known to influence differences in binding specificity. Also, VASP isolated cavity subregions that differ between ligand binding cavities which are essential for differences in binding specificity. As such, VASP should prove a valuable tool in the study of protein-ligand binding specificity.
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Registered trials
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.