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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.
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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
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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Ozvoldik K, Stockner T, Krieger E. YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities. J Chem Inf Model 2023; 63:6177-6182. [PMID: 37782001 PMCID: PMC10598798 DOI: 10.1021/acs.jcim.3c01136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Indexed: 10/03/2023]
Abstract
The industry's transition from three-dimensional (3D) glasses to virtual reality (VR) headsets has left modelers stranded without hardware supply, since walking around and waving arms in a virtual world is a great experience but also very tiring when doing time-intensive modeling work. We present a novel software implementation that uses a VR headset while sitting at a desk in front of the normal screen, which is beamed into the virtual reality together with keyboard, mouse, and chair using the headset's cameras and an extra tracker attached to the seat-back. Compared to 3D glasses, this yields a comparably relaxing but much more immersive workplace and provides additional possibilities such as taking molecules into one's hands, standing up, and walking or teleporting through the models. This VR functionality has been combined with a molecular graphics engine based on Vulkan, a next-generation cross-platform application programming interface (API) for GPUs and the successor of the widely used Open Graphics Library (OpenGL). It is built into the YASARA Model program, which includes many features like small and large molecule builders, electron densities, partial surfaces, contact analysis, coordinate manipulation, and animations. Interactive tutorials are provided to guide modelers into VR and familiarize them with the molecular modeling features. YASARA Model is available for Linux, Windows, Android, and MacOS (the latter without VR) with an introductory video at www.YASARA.org/vr.
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Affiliation(s)
- Kornel Ozvoldik
- Center
for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria
- YASARA
Biosciences GmbH, Wagramer
Str. 25/3/45, 1220 Vienna, Austria
| | - Thomas Stockner
- Center
for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria
| | - Elmar Krieger
- YASARA
Biosciences GmbH, Wagramer
Str. 25/3/45, 1220 Vienna, Austria
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Kong X, Gao P, Wang J, Fang Y, Hwang KC. Advances of medical nanorobots for future cancer treatments. J Hematol Oncol 2023; 16:74. [PMID: 37452423 PMCID: PMC10347767 DOI: 10.1186/s13045-023-01463-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Early detection and diagnosis of many cancers is very challenging. Late stage detection of a cancer always leads to high mortality rates. It is imperative to develop novel and more sensitive and effective diagnosis and therapeutic methods for cancer treatments. The development of new cancer treatments has become a crucial aspect of medical advancements. Nanobots, as one of the most promising applications of nanomedicines, are at the forefront of multidisciplinary research. With the progress of nanotechnology, nanobots enable the assembly and deployment of functional molecular/nanosized machines and are increasingly being utilized in cancer diagnosis and therapeutic treatment. In recent years, various practical applications of nanobots for cancer treatments have transitioned from theory to practice, from in vitro experiments to in vivo applications. In this paper, we review and analyze the recent advancements of nanobots in cancer treatments, with a particular emphasis on their key fundamental features and their applications in drug delivery, tumor sensing and diagnosis, targeted therapy, minimally invasive surgery, and other comprehensive treatments. At the same time, we discuss the challenges and the potential research opportunities for nanobots in revolutionizing cancer treatments. In the future, medical nanobots are expected to become more sophisticated and capable of performing multiple medical functions and tasks, ultimately becoming true nanosubmarines in the bloodstream.
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Affiliation(s)
- Xiangyi Kong
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Peng Gao
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Division of Breast Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Yi Fang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Kuo Chu Hwang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan ROC.
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Konagaya A, Gutmann G, Zhang Y. Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots. J Integr Bioinform 2023; 20:jib-2022-0017. [PMID: 36194394 PMCID: PMC10063180 DOI: 10.1515/jib-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/15/2022] Open
Abstract
This paper describes the design philosophy for our cloud-based virtual reality (VR) co-creation environment (CCE) for molecular modeling. Using interactive VR simulation can provide enhanced perspectives in molecular modeling for intuitive live demonstration and experimentation in the CCE. Then the use of the CCE can enhance knowledge creation by bringing people together to share and create ideas or knowledge that may not emerge otherwise. Our prototype CCE discussed here, which was developed to demonstrate our design philosophy, has already enabled multiple members to log in and touch virtual molecules running on a cloud server with no noticeable network latency via real-time artificial intelligence techniques. The CCE plays an essential role in the rational design of molecular robot parts, which consist of bio-molecules such as DNA and protein molecules.
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Affiliation(s)
- Akihiko Konagaya
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
- Keisen University, 2-10-1, Minamino, Tama, Tokyo, Japan
| | - Gregory Gutmann
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
| | - Yuhui Zhang
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
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Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. The emerging potential of interactive virtual reality in drug discovery. Expert Opin Drug Discov 2022; 17:685-698. [PMID: 35638298 DOI: 10.1080/17460441.2022.2079632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The potential of virtual reality (VR) to contribute to drug design and development has been recognized for many years. A recent advance is to use VR not only to visualize and interact with molecules, but also to interact with molecular dynamics simulations 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful for flexible docking and examining binding processes and conformational changes. AREAS COVERED The authors use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g. in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to using VR controllers to rotate and translate the molecule for enhanced visualization. Here, they describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena. EXPERT OPINION The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together in the same virtual environment - makes modern interactive VR a valuable tool to add to the armory of drug design and development methods.
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Affiliation(s)
- Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Ella M Gale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - David R Glowacki
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
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Kuťák D, Melo L, Schroeder F, Jelic-Matošević Z, Mutter N, Bertoša B, Barišić I. CATANA: an online modelling environment for proteins and nucleic acid nanostructures. Nucleic Acids Res 2022; 50:W152-W158. [PMID: 35544315 PMCID: PMC9252799 DOI: 10.1093/nar/gkac350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.
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Affiliation(s)
- David Kuťák
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia.,Visitlab, Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Lucas Melo
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Fabian Schroeder
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Zoe Jelic-Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Natalie Mutter
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
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