A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
2014
Computer applications in the biosciences : CABIOS
Preserved Fulltext
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2018
Frontiers in Chemistry
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2021
Frontiers in Chemistry
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
Physical Chemistry, Chemical Physics - PCCP
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2020
Computational and Structural Biotechnology Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2021
Life
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2017
Computer graphics forum (Print)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2016
eLife
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2016
Computer graphics forum (Print)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2020
PLoS Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2020
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 16 results