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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Barbora Kozlikova, Eva Sebestova, Vilem Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonin Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry (+3 others)
2014 Computer applications in the biosciences : CABIOS  
CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures.  ...  The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels.  ...  Tunnels/channels calculation: CAVER Analyst integrates CAVER 3.0 for identification of tunnels in static structures and molecular dynamic trajectories.  ... 
doi:10.1093/bioinformatics/btu364 pmid:24876375 fatcat:ytbqgyu3mzf7bdztn256w6imqy

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

2019 Nucleic Acids Research  
Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands' transport through these transport pathways.  ...  The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis.  ...  CONCLUSIONS AND OUTLOOK Caver Web 1.0 is a novel web server for structural and functional analysis of the tunnels and channels in protein structures.  ... 
doi:10.1093/nar/gkz378 pmid:31114897 pmcid:PMC6602463 fatcat:dut73fsarnd75hkbsfg6sar5ea

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

Jingxuan Zhu, Yi Li, Jinzhi Wang, Zhengfei Yu, Ye Liu, Yi Tong, Weiwei Han
2018 Frontiers in Chemistry  
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  ...  with protein structure networks, were employed to theoretically characterize the reasons for the differences in the abilities of the D-fructose catalyzed by the wild-type CbDPEase and Y68I/G109P mutant  ...  ACKNOWLEDGMENTS This work was supported by the Natural Science Foundation of Jilin Province as a major scientific research project [20170101068JC] and was conducted at the High-Performance Computing Center  ... 
doi:10.3389/fchem.2018.00437 pmid:30320068 pmcid:PMC6166005 fatcat:lgsoscigyffyniumw5bpo34jce

Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations

Shitao Zhang, Yi Wang, Lu Han, Xueqi Fu, Song Wang, Wannan Li, Weiwei Han
2021 Frontiers in Chemistry  
In order to explore the conformational changes in the active pocket and unbinding pathway for NtMGAM, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were  ...  2 diabetes since 1990. α-Glucosidases are rather crucial in the human metabolic system and are principally found in families 13 and 31.  ...  ACKNOWLEDGMENTS Amber 16 package was purchased and authorized to use by Jilin University.  ... 
doi:10.3389/fchem.2021.711242 pmid:34527658 pmcid:PMC8435576 fatcat:bdqf42mldnbw3nr5pbv7w4uk7q

Molecular insights into the Patched1 drug efflux inhibitory activity of panicein A hydroquinone: a computational study

Sandra Kovachka, Giuliano Malloci, Attilio Vittorio Vargiu, Stéphane Azoulay, Isabelle Mus-Veteau, Paolo Ruggerone
2021 Physical Chemistry, Chemical Physics - PCCP  
Further, dynamical descriptors of the active and inactive PAH analogues were extracted from microsecond-long all-atom molecular dynamics simulations in water solution.  ...  In this work we combined different computational techniques to gain molecular insights of the inhibitory activity of PAH and some of its active and inactive analogues.  ...  This research has received funding from the French government through the UCAJEDI Investments in the Future project with the reference number  ... 
doi:10.1039/d0cp05719c pmid:33522520 fatcat:l4h4qjxge5azphge3hq5gnise4

Applications of water molecules for analysis of macromolecule properties

Karolina Mitusińska, Agata Raczyńska, Maria Bzówka, Weronika Bagrowska, Artur Góra
2020 Computational and Structural Biotechnology Journal  
The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on  ...  Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.  ...  The most successful ones, such as Mole 2.0 [97] , CAVER 3.0 [98] , and CAVER Analyst 1.0 and 2.0 [99] , [100] , are widely used by the scientific community, predominantly to describe tunnels identified  ... 
doi:10.1016/j.csbj.2020.02.001 pmid:32123557 pmcid:PMC7036622 fatcat:hpqagubnm5czha7gtxiaela5py

Functional Effects In Silico Prediction for Androgen Receptor Ligand-Binding Domain Novel I836S Mutation

Alexey Rayevsky, Dmytro Sirokha, Dariia Samofalova, Dmytro Lozhko, Olexandra Gorodna, Inga Prokopenko, Liudmyla Livshits
2021 Life  
In the present study, we applied a set of computational approaches for the structural analysis of the ligand-binding domains in a wild-type and mutant AR to evaluate the functional impact of the novel  ...  Our analyses provide evidence that I836S causes disruptions of AR protein functionality and development of CAIS clinical features in patients.  ...  From these, Caver Analyst 2.0 calculated the time-dependent volume fluctuations and split the entire tunnel into smaller fragments with a corresponding lifetime.  ... 
doi:10.3390/life11070659 fatcat:avh4haxkubgu3o2azycyuhmgeu

Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey

Tiago Simões, Daniel Lopes, Sérgio Dias, Francisco Fernandes, João Pereira, Joaquim Jorge, Chandrajit Bajaj, Abel Gomes
2017 Computer graphics forum (Print)  
As an exception, a more detailed survey focusing on the visual analysis of biomolecular cavities was recently published [KKL*16], i.e., with a flavor in molecular visualization.  ...  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

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

Yong Wang, Elena Papaleo, Kresten Lindorff-Larsen
2016 eLife  
Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally  ...  Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult.  ...  tool for interactive visualization 539 and analysis of tunnels and channels in protein structures.  ... 
doi:10.7554/elife.17505 pmid:27552057 pmcid:PMC5050026 fatcat:blufywhnlbfrfmekeko3xq2a5u

New Insights Into the Effect of Residue Mutation on the Rotavirus VP1 Function Using Molecular Dynamic Simulations [article]

Nabil Abid, Marco Salemi, Giovanni Chillemi
2020 bioRxiv   pre-print
The results revealed structural fluctuations and secondary structure change of VP1 protein that may alter its function during viral replication/transcription.  ...  Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide.  ...  Analysis of Tunnels in MD Trajectories CAVER Analyst 2.0 [31] was used for the calculation of tunnels in the 10-ns MD simulations of VP1 Native and mutants.  ... 
doi:10.1101/2020.04.08.031443 fatcat:w6qggndnxne5rdpe5sqoj32yzm

Visualization of Biomolecular Structures: State of the Art Revisited

B. Kozlíková, M. Krone, M. Falk, N. Lindow, M. Baaden, D. Baum, I. Viola, J. Parulek, H.-C. Hege
2016 Computer graphics forum (Print)  
Please note that this report does not discuss methods to extract and visualize cavities in biomolecules (e.g. tunnels, pores or channels).  ...  Moreover, the most common sources of molecular structures and molecular dynamics are discussed.  ...  Its successor Ribbons 2.0 [Car91] provided interactive visualization. A current challenge is to improve the efficiency for the interactive visualization of large, dynamic proteins.  ... 
doi:10.1111/cgf.13072 fatcat:offag5kdrnfjjnrqzvrxzxtnuq

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB [article]

Eamonn Reading, Zainab Ahdash, Chiara Fais, Vito Ricci, Xuan Wang-Kan, Elizabeth Grimsey, Jack W Stone, Giuliano Malloci, Andy M Lau, Heather Findlay, Albert Konijnenberg, Paula J Booth (+4 others)
2020 bioRxiv   pre-print
Here, we determine these structural dynamics in the presence of AcrB substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular modelling, drug binding and bacterial susceptibility  ...  Our results provide molecular insight into drug export and inhibition of a major MDR-conferring efflux pump and the important directive role of its dynamics.  ...  CAVER Analyst 2.0: analysis and visualization of channels and tunnels 520 in protein structures and molecular dynamics trajectories.  ... 
doi:10.1101/2020.04.27.063511 fatcat:rzhzn63tbjhjlazd7dive7awpq

Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC [article]

Jakob M Silberberg, Robin A Corey, Lisa Hielkema, Charlott Stock, Phillip James Stansfeld, Cristina Paulino, Inga Haenelt
2021 bioRxiv   pre-print
KdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation.  ...  We unambiguously show that ions are transported via an intersubunit tunnel through KdpA and KdpB.  ...  Radius calculations of the intersubunit tunnel were performed using CAVER Analyst 63 .  ... 
doi:10.1101/2021.05.18.444724 fatcat:g5iepptcczgopfs2qtl2z57yom

Rational design of highly potent broad-spectrum enterovirus inhibitors targeting the nonstructural protein 2C

Lisa Bauer, Roberto Manganaro, Birgit Zonsics, Daniel L. Hurdiss, Marleen Zwaagstra, Tim Donselaar, Naemi G. E. Welter, Regina G. D. M. van Kleef, Moira Lorenzo Lopez, Federica Bevilacqua, Thamidur Raman, Salvatore Ferla (+7 others)
2020 PLoS Biology  
Using computational methods to identify solvent accessible tunnels near the α2 helix in the EV-A71 and PV 2C crystal structures, a conserved binding pocket of the inhibitors is proposed.  ...  Here, we present a structure-activity relationship study of a previously identified compound that targets the 2C protein of EV-A71 and several EV-B species members, but not poliovirus (PV) (EV-C species  ...  Friedrich Förster for providing access to equipment used for purification of recombinant 2C proteins. Author Contributions  ... 
doi:10.1371/journal.pbio.3000904 pmid:33156822 fatcat:u3cvfnot5jae3ej6dhaudgvx74

Pharmacogenetic modeling of human cytochrome P450 2D6; On the force of variation in inducing toxicity

Charleen Gerogette Don
For the analysis of possible access and egress tunnels in the enzyme we employed CAVER 3.0 [26] . CAVER is widely used to identify and characterize transport pathways within enzymes [12, 22, 25] .  ...  Molecular dynamics.  ...  completely replace the in vivo and in vitro approaches for predicting toxicity.  ... 
doi:10.5451/unibas-ep78881 fatcat:yermj4yvdver7dvn3cu4wy6flm
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