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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
A. Jurcik, D. Bednar, J. Byska, SM. Marques, K. Furmanova, L. Daniel, P. Kokkonen, J. Brezovsky, O. Strnad, J. Stourac, A. Pavelka, M. Manak, J. Damborsky, B. Kozlikova,
Jazyk angličtina Země Velká Británie
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
Free Medical Journals
od 1996 do Před 1 rokem
PubMed Central
od 2007
Open Access Digital Library
od 1996-01-01
Medline Complete (EBSCOhost)
od 1998-01-01
Oxford Journals Open Access Collection
od 1985-01-01 do 2022-09-30
Oxford Journals Open Access Collection
od 1985-01-01
ROAD: Directory of Open Access Scholarly Resources
od 1998
- MeSH
- algoritmy MeSH
- konformace proteinů MeSH
- proteinové inženýrství MeSH
- proteiny chemie MeSH
- simulace molekulární dynamiky * MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary information: Supplementary data are available at Bioinformatics online.
Citace poskytuje Crossref.org
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- $a Jurcik, Adam $u Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
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- $a Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary information: Supplementary data are available at Bioinformatics online.
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- $a Bednar, David $u Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic. International Centre for Clinical Research, St. Anne's University Hospital, Brno, Czech Republic.
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- $a Byska, Jan $u Visualization Group, Department of Informatics, University of Bergen, Bergen, Norway.
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- $a Furmanova, Katarina $u Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
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- $a Brezovsky, Jan $u Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic. Department of Gene Expression, Institute of Molecular Biology and Biotechnology Faculty of Biology, Adam Mickiewicz University, Poznan, Poland. International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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- $a Pavelka, Antonin $u Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic.
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- $a Kozlikova, Barbora $u Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
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