ArticleBMC bioinformatics2006
CAVER: a new tool to explore routes from protein clefts, pockets and cavities.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers, 1 of them a synthesis that pooled it.
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Who cites it
217 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Substrate specificity controlled by the exit site of human P4-ATPases, revealed by de novo point mutations in neurological disorders.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Exploring the influence of pore shape on conductance and permeation.Biophysical journal · 2024Article
- Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases.Journal of chemical information and modeling · 2024Article
- Computational studies on the catalytic potential of the double active site for enzyme engineering.Scientific reports · 2024Article
- CageCavityCalc (Journal of chemical information and modeling · 2024Article
- Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein fromBiomolecules · 2023Article
- Mutexa: A Computational Ecosystem for Intelligent Protein Engineering.Journal of chemical theory and computation · 2023Review
- pH-Dependent Binding and Releasing Mechanism of Acetate in the Inner Water Cavity of Heliorhodopsin.Biochemistry · 2023Article
- High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases.Protein science : a publication of the Protein Society · 2023Article
- Intracellular Loop in the Brain Isoforms of Anoctamin 2 Channels Regulates Calcium-dependent Activation.Experimental neurobiology · 2023Article
- Geometric Remodeling of Nitrilase Active Pocket Based on ALF-Scanning Strategy To Enhance Aromatic Nitrile Substrate Preference and Catalytic Efficiency.Applied and environmental microbiology · 2023Article
157 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.
resultsThe algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version.
conclusionThe algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.
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