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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.  ...  of ligands transport through the tunnels.  ... 
doi:10.1093/nar/gkz378 pmid:31114897 pmcid:PMC6602463 fatcat:dut73fsarnd75hkbsfg6sar5ea

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport [article]

Jiří Filipovič, Ondřej Vávra, Jan Plhák, David Bednář, Sérgio M. Marques, Jan Brezovský, Luděk Matyska, Jiří Damborský
2018 arXiv   pre-print
Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm.  ...  CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories.  ...  The authors express their thanks also to infrastructural projects ELIXIR and C4Sys run by the Czech Ministry of Education (LM2015047 and LM2015055) for financial support.  ... 
arXiv:1809.03453v1 fatcat:6eutwhgyrbamrk7zyjo7pozqzu

Interactive exploration of ligand transportation through protein tunnels

Katarína Furmanová, Miroslava Jarešová, Jan Byška, Adam Jurčík, Július Parulek, Helwig Hauser, Barbora Kozlíková
2017 BMC Bioinformatics  
The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses.  ...  This prevents understanding of the ligand transportation and reasoning behind its behavior along the path.  ...  Availability of data and material The software, source code of the algorithms, and source data are available from the corresponding author on reasonable request.  ... 
doi:10.1186/s12859-016-1448-0 pmid:28251878 pmcid:PMC5333178 fatcat:xolz3ws2tvajbg2ehq7ulwcmsu

Visual exploration of large normal mode spaces to study protein flexibility

Pierre Bedoucha, Nathalie Reuter, Helwig Hauser, Jan Byška
2020 Computers & graphics  
Introduction 1 7 tion [ 1 , 2 ] 11712 Proteins come with a large variety of functions, including the2 catalysis of chemical reactions and the transport of molecules 3 in living organisms.  ...  tem is oriented on the datasets involving key protein tunnels 9 for metabolite pathing.  ... 
doi:10.1016/j.cag.2020.05.025 fatcat:nu6zyas5jbarrlm572vjkwcqaq

Nanomanipulation in Biomedical Applications

Chaojian Hou, Dong Sun, Lixin Dong
2021 Current Robotics Reports  
Purpose of Review Progress in nanorobotics over the past decades has dramatically extended our ability to explore the world down to individual molecules/atoms.  ...  This paper overviews the state-of-the-art of the advancements of nanomanipulation and focuses on its application in biomedicine.  ...  Even through cell-level robotassisted OT micromanipulation (automated cell transportation [104] , PID control manipulation [105] , high speed cell transportation [106] , path planning in automated manipulation  ... 
doi:10.1007/s43154-021-00047-4 fatcat:lgapxej5w5fbxdaxku7dg265ri

ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

Matthieu Dreher, Jessica Prevoteau-Jonquet, Mikael Trellet, Marc Piuzzi, Marc Baaden, Bruno Raffin, Nicolas Ferey, Sophie Robert, Sébastien Limet
2014 Faraday discussions  
The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with  ...  Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long-time batch executions).  ...  Samuel Murail and Benoist Laurent for stimulating discussions about the analysis of the GLIC system.  ... 
doi:10.1039/c3fd00142c pmid:25340956 fatcat:u5fjcuzogvefxgjvxep5q7r44e

Protein Dynamics: From Structure to Function [chapter]

Marcus B. Kubitzki, Bert L. de Groot, Daniel Seeliger
2009 From Protein Structure to Function with Bioinformatics  
The use of collective coordinates has proven to be a promising means in this respect, either as a tool for analysis or as part of new sampling algorithms.  ...  Starting from MD simulations, several enhanced sampling algorithms for biomolecular simulations are reviewed in this chapter.  ...  In the simulations, the water molecules were found to rotate by 180 degrees on their path through the pore ( Fig. 9 .5a).  ... 
doi:10.1007/978-1-4020-9058-5_9 fatcat:eldrbt4czbbwhbmhztfwtemj6i


Elizabeth L. Bell, William Finnigan, Scott P. France, Anthony P. Green, Martin A. Hayes, Lorna J. Hepworth, Sarah L. Lovelock, Haruka Niikura, Sílvia Osuna, Elvira Romero, Katherine S. Ryan, Nicholas J. Turner (+1 others)
2021 Nature Reviews Methods Primers  
This Primer discusses the current state-of-the-art methodology in the field, including route design, enzyme discovery, protein engineering and the implementation of biocatalysis in industry.  ...  Its success has been largely due to a rapid expansion of the range of chemical reactions accessible, made possible by advanced tools for enzyme discovery coupled with high-throughput laboratory evolution  ...  Acknowledgements The authors are grateful for funding from the European Research  ... 
doi:10.1038/s43586-021-00044-z fatcat:zzyiptjrrffbznbpqrh2ds24kq

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

Silvio Osella
2021 Nanomaterials  
Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET).  ...  light harvesting and redox-active proteins.  ...  of fuel cells for transport.  ... 
doi:10.3390/nano11020299 pmid:33498961 fatcat:7xj7f2vmlvb5pebxlzj7uje3gm

Protein DynamicsProtein Dynamics : From Structure to Function [chapter]

Marcus B. Kubitzki, Bert L. de Groot, Daniel Seeliger
2017 From Protein Structure to Function with Bioinformatics  
The use of collective coordinates has proven to be a promising means in this respect, either as a tool for analysis or as part of new sampling algorithms.  ...  Starting from MD simulations, several enhanced sampling algorithms for biomolecular simulations are reviewed in this chapter.  ...  The main protein-water interaction sites are the ar/R region and the NPA site ). In the simulations, the water molecules were found to rotate by 180°on their path through the pore (Fig. 12 .5a).  ... 
doi:10.1007/978-94-024-1069-3_12 fatcat:5jyf4drvsndmdovo6ka2hpmdmq

Molecular insights into the mechanisms of transport and energy coupling in membrane transport proteins

Tao Jiang
2017 Zenodo  
Membrane transport proteins are the main gatekeepers controlling the traffic of molecules in and out the cell.  ...  These findings provide structural details of anion binding in ClC-ec1 and reveal a putative atomic-level mechanism for the decoupling of H+ transport to the transport of anions other than Cl [...]  ...  The radius profile of the ClC-ec1 Cl − transport tunnel, calculated using the program HOLE [215] , shows an extracellular bottleneck with a minimum radius of ∼0.2Å (Fig. 5.5) .  ... 
doi:10.5281/zenodo.4737779 fatcat:asb7x6f7tzdv5lgc6drl3wmfym

The data center of tomorrow is made up of heterogeneous accelerators [article]

Xavier Vasques
2021 arXiv   pre-print
The data center of tomorrow is a data center made up of heterogeneous systems, which will run heterogeneous workloads. The systems will be located as close as possible to the data.  ...  Like an orchestra conductor, the hybrid cloud will make it possible to set these systems to music thanks to a layer of security and intelligent automation.  ...  For example, in 71 cities, the number of candidate paths is greater than 5 × 10^80.  ... 
arXiv:2003.10950v2 fatcat:f6ri4hc465etplidhepgxrouaa

Molecular Information Technology

Klaus-Peter Zauner
2005 Critical reviews in solid state and materials sciences  
Present applications of molecules range from organic semiconductor materials for low-cost circuits to genetically modified proteins for commercial imaging equipment.  ...  This article reviews current directions in the use of bulk and single molecules for information processing.  ...  inversion [184, 182, 188] , and can be used for path planning [189] .  ... 
doi:10.1080/10408430590918387 fatcat:cg62axmewndhpdf2uo22knwvua

Toward an integrated software platform for systems pharmacology

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, Hiroaki Kitano
2013 Biopharmaceutics & drug disposition  
A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost  ...  This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context.  ...  Conflict of Interest The authors have declared that there is no conflict of interest. Further Information  ... 
doi:10.1002/bdd.1875 pmid:24150748 pmcid:PMC4253131 fatcat:l4dvxrd4qzeqro75ysop35j4b4

How to Build a Biological Machine Using Engineering Materials and Methods

Alex Ellery
2020 Biomimetics  
We then examine these lessons to explore the construction of a self-replicating machine using a universal constructor. It is through the universal constructor that the actuator emerges as critical.  ...  of motors in biology viewed from the perspective of engineering (in the Feynman spirit of "what I cannot create, I cannot understand").  ...  Acknowledgments: I would like to thank Oak Ridge National Laboratory for their 3D printed rare earth magnets. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biomimetics5030035 pmid:32722540 pmcid:PMC7558640 fatcat:dti5lsql7faptgrruyxetbn3qy
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