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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
2012
PLoS Computational Biology
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Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. ...
of Technology, Czech Republic) for providing the scripts for visualization of pathway dynamics in VMD and PyMOL software. ...
Rebecca Wade (Heidelberg Institute for Theoretical Studies, Germany) for providing data for beta-testing of CAVER 3.0, Jan Stourac (Gymnazium Brno-Reckovice, Czech Republic) and Jaroslav Bendl (Brno University ...
doi:10.1371/journal.pcbi.1002708
pmid:23093919
pmcid:PMC3475669
fatcat:3z5ldoikgbfg7paoo5abyrskji
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
2007
Biotechnology Journal
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Here we present examples from the use of CAVER for identification of tunnels in two protein families studied in our laboratories. ...
[51] analyzed using CAVER (PDB ID 1CQW). Two preferred paths with the population 64% and 36%, respectively, were assigned as the upper tunnel and the slot [14] . ...
doi:10.1002/biot.200600208
pmid:17183511
fatcat:xdry6mpfrfdrfbf4ozikjfi4ya
Software tools for identification, visualization and analysis of protein tunnels and channels
2013
Biotechnology Advances
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MetaCentrum is acknowledged for providing access to computing facilities, supported by the Ministry of Education of the Czech Republic (LM2010005). ...
.), the Grant Agency of the Czech Republic (P202/10/1435 to A.P., P503/12/0572 to J.D.) and the Grant Agency of the Czech Academy of Sciences (IAA401630901 to J.B. and J.D.). ...
To examine the dynamical nature of tunnels, the tunnel-intersecting residues of mammalian CYP450 isoforms were analyzed. The results of this analysis enabled the definition of gating models. ...
doi:10.1016/j.biotechadv.2012.02.002
pmid:22349130
fatcat:qm6uw2qdfvbcbms4niik5tbqnu
Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins
2019
Eurographics Workshop on Visual Computing for Biomedicine
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We present a novel abstract visualization for the binding sites of proteins. Binding sites play an essential role in enzymatic reactions and are, thus, often investigated in structural biology. ...
Molecular surface visualizations can help to analyze the accessibility of binding sites, but are typically prone to visual clutter. ...
Sanner for providing his MSMS software and B. Kozlíková and colleagues for providing the CAVER Analyst software package. ...
doi:10.2312/vcbm.20191248
dblp:conf/vcbm/SchatzKBFPE19
fatcat:c2tpzj6bavbrrhfn7e5f2zepma
Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations
2019
International Journal of Molecular Sciences
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In addition, CAVER 3.0 analysis revealed that β-valienamine could make the tunnel of BtrR wider and straight, which was propitious to the removal of products from BtrR. ...
Steered MD simulation results showed that valienamine interacted with more residues in the tunnel during dissociation compared with β-valienamine, resulting in the need for a stronger force to be acquired ...
of Jilin University. ...
doi:10.3390/ijms20051188
fatcat:6h2skd75xfhoralt2lqvq5xciq
Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores
2009
Biophysical Journal
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The correctness and accuracy of the algorithm is verified on a constructed set of proteins and used to analyze large sets of real proteins. ...
We describe a new algorithm, CHUNNEL, to automatically find, characterize, and display tunnels or pores in proteins. ...
Funding for K.A.S. and R.G.C. was provided by NIH GM48130. ...
doi:10.1529/biophysj.108.135970
pmid:18849407
pmcid:PMC2716472
fatcat:n245zgnr5nbxzmbibt2oczplxq
Protein Tunnel Reprojection for Physico-Chemical Property Analysis
[article]
2017
Eurographics Workshop on Visual Computing for Biomedicine
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Consequently, domain scientists are interested in understanding properties relevant for binding interactions inside molecular tunnels. ...
Unfortunately, when inspecting a 3D representation of the molecule under investigation, tunnels are difficult to analyze due to occlusion issues. ...
The first algorithms for protein tunnel computation were based on grid approaches, such as the first version of CAVER tool published by Petrek et al. [POB * 06]. ...
doi:10.2312/vcbm.20171231
dblp:conf/vcbm/MalzahnKR17
fatcat:waaft2jp35h6bfoxtwveuoqb4e
Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers
2021
Frontiers in Molecular Biosciences
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We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. ...
Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. ...
Tunnel Analysis The Caver 3.03 beta software (Chovancova et al., 2012) was used for the effective analysis of tunnels in structures derived from the molecular dynamics trajectories. ...
doi:10.3389/fmolb.2021.710623
pmid:34604302
pmcid:PMC8479113
fatcat:ld32cgqqmbh3tjs3lzv4codeie
Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae
2018
Frontiers in Chemistry
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In our study, a battery of molecular modeling methods [homology modeling, adaptive steered molecular dynamics (ASMD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GB/SA)], combined ...
It made the tunnel have an open state and resulted in the stable donor-π interactions between D-fructose and the benzene rings around 18Å. ...
of Jilin University. ...
doi:10.3389/fchem.2018.00437
pmid:30320068
pmcid:PMC6166005
fatcat:lgsoscigyffyniumw5bpo34jce
Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering
2020
International Journal of Molecular Sciences
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To help protein engineers to harness benefits of considering dynamics in their designs, we surveyed new tools developed for analyses of conformational ensembles in order to select engineering hotspots ...
With the tremendous progress in more powerful computer hardware and more efficient algorithms, some of in silico tools and methods have started to apply the more realistic description of proteins as their ...
For CaverDock operation, tunnels must be represented as sequences of spheres for each given conformation of a macromolecule. Such input data can be easily generated by CAVER 3.0 software [86] . ...
doi:10.3390/ijms21082713
pmid:32295283
fatcat:jp4p37apzvdyxpyimi3jerblxa
Theoretical and Computational Research on Halide Ion Release Channel of Haloalcohol Dehalogenase From Agrobacterium Radiobacter AD1
2014
OALib
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This article includes pure theoretical and computational studies using classic molecular dynamics simulations, random acceleration molecular dynamics simulations and specialized toolkit MOLE 2.0 for predicting ...
These enzymes exhibit a huge potential in the synthesis of chiral pharmaceutical intermediates. ...
Two mostly used tools in this field CAVER and MOLE both 67 developed by researchers from Czech Republic have proved to be a success in this field. , And due 68 to the difference of the algorithms adopted ...
doi:10.4236/oalib.preprints.1200045
fatcat:mvxpjjygh5c55i7urckgnltbjy
Recent advances in user-friendly computational tools to engineer protein function
2020
Briefings in Bioinformatics
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Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. ...
Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. ...
It requires pre-computed tunnels for a given macromolecule by software such as CAVER 3.02 [108] . ...
doi:10.1093/bib/bbaa150
pmid:32743637
pmcid:PMC8138880
fatcat:4dmqbggn2nbsxcfzd4jg4rq6zy
Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey
2017
Computer graphics forum (Print)
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Detecting and analyzing protein cavities provides significant information about active sites for biological processes (e.g., protein-protein or protein-ligand binding) in molecular graphics and modeling ...
Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels, and grooves on the surface of a given protein. ...
Subsequent upgrades of the CAVER software were introduced in CAVER 2.0 [MBS08] , in which the axis-aligned grid was replaced by the Voronoi diagram to describe the skeleton of tunnels within the structure ...
doi:10.1111/cgf.13158
pmid:29520122
pmcid:PMC5839519
fatcat:5t4rhndtunhvtmkm32niknst7i
Molecular insights into the Patched1 drug efflux inhibitory activity of panicein A hydroquinone: a computational study
2021
Physical Chemistry, Chemical Physics - PCCP
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Further, dynamical descriptors of the active and inactive PAH analogues were extracted from microsecond-long all-atom molecular dynamics simulations in water solution. ...
for PTCH1. ...
R. thank Andrea Bosin and Giovanni Serra (Cagliari) for technical assistance. The Authors acknowledge Méliné Simsir (Nice) for sharing her knowledge and experience about PTCH1 efflux. ...
doi:10.1039/d0cp05719c
pmid:33522520
fatcat:l4h4qjxge5azphge3hq5gnise4
Implicit surfaces for interactive graph based cavity analysis of molecular simulations
2012
2012 IEEE Symposium on Biological Data Visualization (BioVis)
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The analysis is often concerned with visual identification of binding sites of ligands to a host macromolecule. ...
Molecular surfaces provide a suitable way to analyze and to study the evolution and interaction of molecules. ...
Additionally, we would like to thank Helwig Hauser and Visualization group in Bergen for useful ideas and feedback. ...
doi:10.1109/biovis.2012.6378601
dblp:conf/biovis/ParulekTRV12
fatcat:tykp5dp3sffy5jcsjttoaoa3zi
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