ArticleBMC bioinformatics2015
CHEXVIS: a tool for molecular channel extraction and visualization.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
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- Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21.Nature structural & molecular biology · 2023Article
- Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.International journal of molecular sciences · 2022Article
- Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands.PloS one · 2022Article
- The computational analyses, molecular dynamics of fatty-acid transport mechanism to the CD36 receptor.Scientific reports · 2021Article
- Pannexin 1 mutation found in melanoma tumor reduces phosphorylation, glycosylation, and trafficking of the channel-forming protein.Molecular biology of the cell · 2021Article
- In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor.Computers in biology and medicine · 2020Article
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- Non-adaptive Evolution of Trimeric Autotransporters inFrontiers in microbiology · 2020Article
- Molecular Cavity Topological Representation for Pattern Analysis: A NLP Analogy-Based Word2Vec Method.International journal of molecular sciences · 2019Article
- Structure of a Tc holotoxin pore provides insights into the translocation mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Common architecture of Tc toxins from human and insect pathogenic bacteria.Science advances · 2019Article
- Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae.The FEBS journal · 2019Article
- Cryo-EM structure of the ClpXP protein degradation machinery.Nature structural & molecular biology · 2019Article
- Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.Nucleic acids research · 2019Article
- GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm.International journal of molecular sciences · 2019Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundUnderstanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for extracting, storing, and analyzing protein channels are required to support such studies. Further, there is a need for an integrated framework that supports computation of the channels, interactive exploration of their structure, and detailed visual analysis of their properties.
resultsWe describe a method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. We describe methods for effective visualization of the channels and their profiles. These methods and the visual analysis framework are implemented in a software tool, CHEXVIS. We apply the method on a number of known channel containing proteins to extract pore features. Results from these experiments on several proteins show that CHEXVIS performance is comparable to, and in some cases, better than existing channel extraction techniques. Using several case studies, we demonstrate how CHEXVIS can be used to study channels, extract their properties and gain insights into molecular function.
conclusionCHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels. The CHEXVIS web-server is freely available at http://vgl.serc.iisc.ernet.in/chexvis/ . The web-server is supported on all modern browsers with latest Java plug-in.
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