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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor (+2 others)
2012 PLoS Computational Biology  
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

Jiří Damborský, Martin Petřek, Pavel Banáš, Michal Otyepka
2007 Biotechnology Journal  
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

Jan Brezovsky, Eva Chovancova, Artur Gora, Antonin Pavelka, Lada Biedermannova, Jiri Damborsky
2013 Biotechnology Advances  
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

Karsten Schatz, Michael Krone, Tabea L. Bauer, Valerio Ferrario, Jürgen Pleiss, Thomas Ertl
2019 Eurographics Workshop on Visual Computing for Biomedicine  
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

Ye Liu, Youzhong Wan, Jingxuan Zhu, Muxin Li, Zhengfei Yu, Jiarui Han, Zuoming Zhang, Weiwei Han
2019 International Journal of Molecular Sciences  
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

Ryan G. Coleman, Kim A. Sharp
2009 Biophysical Journal  
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]

Jan Malzahn, Barbora Kozlíková, Timo Ropinski
2017 Eurographics Workshop on Visual Computing for Biomedicine  
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

Khair Bux, Xiayu Shen, Muhammad Tariq, Junqi Yin, Syed Tarique Moin, Debsindhu Bhowmik, Shozeb Haider
2021 Frontiers in Molecular Biosciences  
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

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  ...  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

Bartłomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Jan Brezovsky
2020 International Journal of Molecular Sciences  
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

Yunwen Tao
2014 OALib  
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

Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovsky
2020 Briefings in Bioinformatics  
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

Tiago Simões, Daniel Lopes, Sérgio Dias, Francisco Fernandes, João Pereira, Joaquim Jorge, Chandrajit Bajaj, Abel Gomes
2017 Computer graphics forum (Print)  
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

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.  ...  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

Julius Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola
2012 2012 IEEE Symposium on Biological Data Visualization (BioVis)  
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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