1
|
Belghit H, Spivak M, Dauchez M, Baaden M, Jonquet-Prevoteau J. From complex data to clear insights: visualizing molecular dynamics trajectories. FRONTIERS IN BIOINFORMATICS 2024; 4:1356659. [PMID: 38665177 PMCID: PMC11043564 DOI: 10.3389/fbinf.2024.1356659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
Collapse
Affiliation(s)
- Hayet Belghit
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Mariano Spivak
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Marc Baaden
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
| | | |
Collapse
|
2
|
Vijh RK, Sharma U, Kapoor P, Raheja M, Arora R, Ahlawat S, Dureja V. Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds. Gene 2023; 885:147691. [PMID: 37544337 DOI: 10.1016/j.gene.2023.147691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/06/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Goats are the supporting pillars of rural economy contributing significantly to meat and milk production in India. It is a species targeted for fulfilling the interdependent goals of poverty reduction and creation of employment for supporting the rural income. The increased demand for goat products necessitates their genetic characterization and improvement to augment the production of native breeds. Bi-allelic, genome wide, densely placed single nucleotide polymorphism (SNP) markers are most suitable for this purpose. This paper describes the design and validation of an Affymetrix Axiom-based high-density (HD) SNP chip for goats. The array was designed using a panel of 225 samples from 15 diverse goat breeds of India. In total, more than 38 million high quality SNPs were subjected to stringent filtering and 626,975 SNPs were finally tiled on the array. The average coverage of SNPs in our chip is one SNP per four kilobase (kb), providing a denser coverage of the goat genome than previously available arrays. The HD chip (Axiom_Cahi) was validated by genotyping 443 samples from 26 indigenous goat breeds/populations. The results revealed 95.83% markers to be highly informative and polymorphic in Indian goats. Multivariate analysis indicated population structuring, as 15 breeds could be segregated using the designed array. Phylogenetic analysis suggested stratification of breeds by geographic proximity. This HD SNP chip for goats is a valuable resource for genomic selection, genome wide association as well as population genetic studies in goats.
Collapse
Affiliation(s)
- Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Prerna Kapoor
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Meenal Raheja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Vandana Dureja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| |
Collapse
|
3
|
Kampfrath M, Staritzbichler R, Hernández GP, Rose AS, Tiemann JKS, Scheuermann G, Wiegreffe D, Hildebrand PW. MDsrv: visual sharing and analysis of molecular dynamics simulations. Nucleic Acids Res 2022; 50:W483-W489. [PMID: 35639717 PMCID: PMC9252803 DOI: 10.1093/nar/gkac398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, based on Mol*, MDsrv now provides faster and more efficient visualization of even large trajectories compared to its predecessor tool NGL.
Collapse
Affiliation(s)
- Michelle Kampfrath
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany
| | - René Staritzbichler
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Guillermo Pérez Hernández
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | | | - Johanna K S Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark
| | - Gerik Scheuermann
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany
| | - Daniel Wiegreffe
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany
| | - Peter W Hildebrand
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany
| |
Collapse
|
4
|
Cassidy KC, Šefčík J, Raghav Y, Chang A, Durrant JD. ProteinVR: Web-based molecular visualization in virtual reality. PLoS Comput Biol 2020; 16:e1007747. [PMID: 32231351 PMCID: PMC7147804 DOI: 10.1371/journal.pcbi.1007747] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/10/2020] [Accepted: 02/25/2020] [Indexed: 01/21/2023] Open
Abstract
Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/. Proteins are microscopic machines that help maintain, defend, and regulate cells. Properly understanding the three-dimensional structures of these machines–as well as the small molecules that interact with them–can advance scientific fields ranging from basic molecular biology to drug discovery. Virtual reality (VR) is a powerful tool for studying protein structures. But many current systems for viewing molecules in VR, though effective, have challenging usability limitations. We have created a new web application called ProteinVR that overcomes these challenges. ProteinVR enables VR molecular visualization in users’ browsers, without requiring them to install a separate program or plugin. It runs on a broad range of desktop, laptop, and mobile devices. For users without VR headsets, ProteinVR leverages mobile-device orientation sensors or video-game-style keyboard navigation to provide an immersive experience. We release ProteinVR as open-source software and have posted a working version at http://durrantlab.com/pvr/.
Collapse
Affiliation(s)
- Kevin C Cassidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jan Šefčík
- Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic
| | - Yogindra Raghav
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Chang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|