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Lin Z, Yang Z, Ye X. Immersive Experience and Climate Change Monitoring in Digital Landscapes: Evidence from Somatosensory Sense and Comfort. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3332. [PMID: 36834034 PMCID: PMC9966150 DOI: 10.3390/ijerph20043332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In this study, the virtual engine software (Unity 2019, Unity Software Inc., San Francisco, California, the U.S.) was used to generate a digital landscape model, forming a virtual immersive environment. Through field investigation and emotional preference experiments, the ancient tree ecological area and the sunlight-exposed area were respectively monitored, and the somatosensory comfort evaluation model was established. The subjects showed the highest degree of interest in the ancient tree ecological area after landscape roaming experience, and the mean variance in SC fluctuation was 13.23% in experiments. The subjects were in a low arousal state and had a significant degree of interest in the digital landscape roaming scene, and there was a significant correlation between positive emotion, somatosensory comfort and the Rating of Perceived Exertion index; moreover, the somatosensory comfort of the ancient tree ecological area was higher than that of the sunlight-exposed area. Meanwhile, it was found that somatosensory comfort level can effectively distinguish the comfort level between the ancient tree ecological area and the sunlight-exposed area, which provides an important basis for monitoring extreme heat. This study concludes that, in terms of the goal of harmonious coexistence between human and nature, the evaluation model of somatosensory comfort can contribute to reducing people's adverse views on extreme weather conditions.
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Affiliation(s)
- Zhengsong Lin
- Virtual Landscape Design Lab, School of Art and Design, Wuhan Institute of Technology, Wuhan 430205, China; (Z.L.); (Z.Y.)
| | - Ziqian Yang
- Virtual Landscape Design Lab, School of Art and Design, Wuhan Institute of Technology, Wuhan 430205, China; (Z.L.); (Z.Y.)
| | - Xinyue Ye
- Department of Landscape Architecture and Urban Planning, Center for Geospatial Sciences, Applications and Technology, TAMIDS Design and Analytics Lab for Urban Artificial Intelligence, Texas A&M University, College Station, TX 77840, USA
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Iakovou G, Laycock SD, Hayward S. Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT. J Chem Inf Model 2022; 62:5855-5861. [PMID: 36398912 DOI: 10.1021/acs.jcim.2c01274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to structure-based drug design (SBDD) and educating students about biomolecular interactions. For SBDD, it enables expertise and intuition to be brought to bear in the drug design process. In education, it can teach students about the most basic level of biomolecular function. Here, we introduce DockIT for virtual reality (VR) that uses a VR headset and hand-held controllers. Using the method of linear response on explicit solvent molecular dynamics simulations, DockIT can model both global and local conformational changes within the receptor due to forces of interaction with the ligand. It has real-time flexible molecular surface rendering and can show the real-time formation and breaking of hydrogen bonds, both between the ligand and receptor and within the receptor itself as it smoothly changes conformation.
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Affiliation(s)
- Georgios Iakovou
- Digital Platforms, Aviva Plc, Norwich, NorfolkNR1 3NS, United Kingdom.,School of Computing Sciences, University East Anglia, NorwichNR4 7TJ, United Kingdom
| | - Stephen D Laycock
- School of Computing Sciences, University East Anglia, NorwichNR4 7TJ, United Kingdom
| | - Steven Hayward
- School of Computing Sciences, University East Anglia, NorwichNR4 7TJ, United Kingdom
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Plateau-Holleville C, Guionnière S, Boyer B, Jiménez-Garcia B, Levieux G, Mérillou S, Maria M, Montes M. UDock2: interactive real-time multi-body protein-protein docking software. Bioinformatics 2022; 39:btad609. [PMID: 37792496 PMCID: PMC10938049 DOI: 10.1093/bioinformatics/btad609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/10/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023] Open
Abstract
MOTIVATION Protein-protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software. RESULTS This article presents an interactive multi-body protein-protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties. AVAILABILITY AND IMPLEMENTATION UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.
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Affiliation(s)
| | - Simon Guionnière
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | - Benjamin Boyer
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | | | - Guillaume Levieux
- CEDRIC, EA 4626, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | | | - Maxime Maria
- XLIM, UMR CNRS 7252, University of Limoges, 87000 Limoges, France
| | - Matthieu Montes
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
- Institut Universitaire de France (IUF), Paris 75005, France
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Lanrezac A, Férey N, Baaden M. Wielding the power of interactive molecular simulations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- André Lanrezac
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
| | - Nicolas Férey
- CNRS, Laboratoire interdisciplinaire des sciences du numérique Université Paris‐Saclay Orsay France
| | - Marc Baaden
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
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Iakovou G, Alhazzazi M, Hayward S, Laycock SD. DockIT: a tool for interactive molecular docking and molecular complex construction. Bioinformatics 2020; 36:5698-5700. [PMID: 33367508 DOI: 10.1093/bioinformatics/btaa1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/30/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY DockIT is a tool that has a unique set of physical and graphical features for interactive molecular docking. It enables the user to bring a ligand and a receptor into a docking pose by controlling relative position and orientation, either with a mouse and keyboard, or with a haptic device. Atomic interactions are modelled using molecular dynamics-based force-fields with the force on the ligand being felt on a haptic device. Real-time calculation and display of intermolecular hydrogen bonds and multipoint collision detection either using maximum force or maximum atomic overlap, mean that together with the ability to monitor selected intermolecular atomic distances, the user can find physically feasible docking poses that satisfy distance constraints derived from experimental methods. With these features and the ability to output and reload docked structures it can be used to accurately build up large multi-component molecular systems in preparation for molecular dynamics simulation. AVAILABILITY AND IMPLEMENTATION DockIT is available free of charge for non-commercial use at http://www.haptimol.co.uk/downloads.htm. It requires a windows computer with GPU that supports OpenCL 1.2 and OpenGL 4.0. It may be used with a mouse and keyboard, or a haptic device from 3DSystems.
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Affiliation(s)
- Georgios Iakovou
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K.,Digital Engineering, Aviva Plc, Norwich, NR1 3NS, U.K Norfolk
| | - Mousa Alhazzazi
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
| | - Steven Hayward
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
| | - Stephen D Laycock
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
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Matthews N, Kitao A, Laycock S, Hayward S. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. J Chem Inf Model 2019; 59:2900-2912. [DOI: 10.1021/acs.jcim.9b00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nick Matthews
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, M6-13, Meguro, Tokyo 152-8550, Japan
| | - Stephen Laycock
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Steven Hayward
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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Liu XH, Wang T, Lin JP, Wu MB. Using virtual reality for drug discovery: a promising new outlet for novel leads. Expert Opin Drug Discov 2018; 13:1103-1114. [PMID: 30457399 DOI: 10.1080/17460441.2018.1546286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Introduction: Virtual reality (VR) environments are increasingly being used by researchers in various fields in addition to being increasingly integrated into various areas of human life, ranging from videogames to different industrial uses. VR can be used to create interactive and multimodal sensory stimuli and thus offers unique advantages over other computer-based approaches for scientific research and molecular-level applications. Consequently, VR is starting to be used in novel drug development, such as in drug discovery, and rational drug design. Areas covered: In this review, the authors discuss the basic development of VR technology, including the available hardware and software. The latest advances of VR technology in novel drug development are then detailed, and the VR programs that can be applied in relevant studies are highlighted. Expert opinion: VR will lead to a revolution in pharmaceutical development. However, there are still obstacles to the successful and extensive application of VR to drug development, including the demand for further improvements to the available hardware and software and the various limitations described with regard to accuracy and precision. As technology continues to improve, the barriers to the widespread adoption of VR will diminish and VR technologies will play an increasingly important role in novel drug development.
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Affiliation(s)
- Xiao-Huan Liu
- a School of Biological Science , Jining Medical University , Jining , China
| | - Tao Wang
- a School of Biological Science , Jining Medical University , Jining , China.,b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China
| | - Jian-Ping Lin
- b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China
| | - Mian-Bin Wu
- b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China.,c Zhejiang Key Laboratory of Antifungal Drugs , Taizhou , China
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Assemble-And-Match: A Novel Hybrid Tool for Enhancing Education and Research in Rational Structure Based Drug Design. Sci Rep 2018; 8:849. [PMID: 29339792 PMCID: PMC5770410 DOI: 10.1038/s41598-017-18151-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/05/2017] [Indexed: 11/08/2022] Open
Abstract
Rational drug design is the process of finding new medication that can activate or inhibit the biofunction of a target molecule by binding to it and forming a molecular complex. Here, shape and charge complementarities between drug and target are key. To help find effective drug molecules out of a huge pool of possibilities, physical and computer aided tools have been developed. Former offers a tangible experience of the molecular interactions yet lacks measurement and evaluation capabilities. Latter enables accurate and fast evaluations, but does not deliver the interactive tangible experience of physical models. We introduce a novel hybrid model called "Assemble-And-Match" where, we enhance and combine the unique features of the two categories. Assemble-And-Match works based on fabrication of customized molecular fragments using our developed software and a 3D printer. Fragments are hinged to each other in different combinations and form flexible peptide chains, conformable to tertiary structures, to fit in the binding pocket of a (3D printed) target molecule. Through embedded measurement marks, the molecular model is reconstructed in silico and its properties are evaluated. We expect Assemble-And-Match tool can enable combination of visuospatial perception with in silico computational power to aid research and education in drug design.
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9
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Iakovou G, Hayward S, Laycock SD. Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. J Chem Inf Model 2017; 57:1142-1152. [DOI: 10.1021/acs.jcim.7b00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgios Iakovou
- School of Computing Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Steven Hayward
- School of Computing Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Stephen D. Laycock
- School of Computing Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
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10
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Marzo-Mas A, Barbier P, Breuzard G, Allegro D, Falomir E, Murga J, Carda M, Peyrot V, Marco JA. Interactions of long-chain homologues of colchicine with tubulin. Eur J Med Chem 2016; 126:526-535. [PMID: 27915168 DOI: 10.1016/j.ejmech.2016.11.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 01/30/2023]
Abstract
Several colchicine analogues in which the N-acetyl residue has been replaced by aliphatic, straight-chain acyl moieties, have been synthesized. These compounds show high cytotoxic activity at the nanomolar level against the tumoral cell lines HT-29, MCF-7 and A549. Some of them exhibit activities in the picomolar range against the HT-29 line and are thus two to three orders of magnitude more cytotoxic than colchicine. In this specific cell line, the activities were found to be closely related to the length of the acyl carbon chain, an increase in the latter giving rise to an increase in the cytotoxicity with a maximum in the range of 10-12 carbon atoms, followed by a decrease in activity with still longer chains. Some of the compounds inhibit microtubule assembly and induce the formation of abnormal polymers and present in most cases better apparent affinity constants than colchicine. In addition, at IC50 concentrations the analogues block the cell cycle of A549 cells in the G2/M phase. Molecular docking studies suggest that, while interactions of the colchicine analogues with the colchicine binding site at β-tubulin are still present, the increase in the acyl chain length leads to the progressive development of new interactions, not present in colchicine itself, with the neighboring α-tubulin subunit. Indeed, sufficiently long acyl chains span the intradimer interface and contact with a hydrophobic groove in α-tubulin. It is worth noting that some of the compounds show cytotoxicity at concentrations three orders of magnitude lower than colchicine. Their pharmacological use in cancer therapy could possibly be performed with lower dosages and be thus endowed with less acute toxicity problems than in the case of colchicine.
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Affiliation(s)
- Ana Marzo-Mas
- Depart. de Q. Inorgánica y Orgánica, Univ. Jaume I, E-12071 Castellón, Spain
| | - Pascale Barbier
- Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Gilles Breuzard
- Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Diane Allegro
- Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Eva Falomir
- Depart. de Q. Inorgánica y Orgánica, Univ. Jaume I, E-12071 Castellón, Spain
| | - Juan Murga
- Depart. de Q. Inorgánica y Orgánica, Univ. Jaume I, E-12071 Castellón, Spain.
| | - Miguel Carda
- Depart. de Q. Inorgánica y Orgánica, Univ. Jaume I, E-12071 Castellón, Spain
| | - Vincent Peyrot
- Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France.
| | - J Alberto Marco
- Depart. de Q. Orgánica, Univ. de Valencia, E-46100 Burjassot, Valencia, Spain
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Abstract
The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.
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Iakovou G, Hayward S, Laycock SD. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics. J Mol Graph Model 2015; 61:1-12. [DOI: 10.1016/j.jmgm.2015.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022]
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Hirst JD, Glowacki DR, Baaden M. Molecular simulations and visualization: introduction and overview. Faraday Discuss 2014; 169:9-22. [DOI: 10.1039/c4fd90024c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Anthopoulos A, Pasqualetto G, Grimstead I, Brancale A. Haptic-driven, interactive drug design: implementing a GPU-based approach to evaluate the induced fit effect. Faraday Discuss 2014; 169:323-42. [DOI: 10.1039/c3fd00139c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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15
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Iakovou G, Hayward S, Laycock S. A real-time proximity querying algorithm for haptic-based molecular docking. Faraday Discuss 2014; 169:359-77. [DOI: 10.1039/c3fd00123g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware.
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Affiliation(s)
- Georgios Iakovou
- School of Computing Sciences
- University of East Anglia
- Norwich, UK
| | - Steven Hayward
- School of Computing Sciences
- University of East Anglia
- Norwich, UK
| | - Stephen Laycock
- School of Computing Sciences
- University of East Anglia
- Norwich, UK
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16
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Anthopoulos A, Grimstead I, Brancale A. GPU-accelerated molecular mechanics computations. J Comput Chem 2013; 34:2249-60. [DOI: 10.1002/jcc.23384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 11/06/2022]
Affiliation(s)
| | - Ian Grimstead
- School of Computer Science; Cardiff University; Cardiff; CF24 3AA; United Kingdom
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Cardiff; CF10 3NB; United Kingdom
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Dalkas GA, Vlachakis D, Tsagkrasoulis D, Kastania A, Kossida S. State-of-the-art technology in modern computer-aided drug design. Brief Bioinform 2012; 14:745-52. [DOI: 10.1093/bib/bbs063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Haptic-driven applications to molecular modeling: state-of-the-art and perspectives. Future Med Chem 2012; 4:1219-28. [DOI: 10.4155/fmc.12.60] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Drug design is a creative process that combines different scientific expertise. With the development of increasingly powerful computers, disciplines such as molecular modeling and, in particular, drug design, are becoming an important component of drug discovery. However, modern software often limits the user interaction with the computer calculation, reducing the potential for researchers to use their knowledge in the design process. For this reason, interactive methodologies have been investigated in recent years. In particular, haptic-driven simulators offer the possibility for users to drive and control the modeling simulations, efficiently combining human knowledge and computational power. In this article, we will discuss the state-of-the-art and future perspectives of such methodologies.
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Massarotti A, Coluccia A, Sorba G, Silvestri R, Brancale A. De novo computer-aided design of novel antiviral agents. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e175-e226. [PMID: 24064311 DOI: 10.1016/j.ddtec.2011.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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20
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O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform 2011; 3:33. [PMID: 21982300 PMCID: PMC3198950 DOI: 10.1186/1758-2946-3-33] [Citation(s) in RCA: 4961] [Impact Index Per Article: 381.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 10/07/2011] [Indexed: 02/08/2023] Open
Abstract
Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.
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Affiliation(s)
- Noel M O'Boyle
- University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Pittsburgh, PA 15217, USA.
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21
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O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform 2011. [PMID: 21982300 DOI: 10.1186/1758-2946-3-33.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. RESULTS We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. CONCLUSIONS Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.
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Affiliation(s)
- Noel M O'Boyle
- University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Pittsburgh, PA 15217, USA.
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Zonta N, Coluccia A, Brancale A. Advanced in silico Approaches in Antiviral Research. ACTA ACUST UNITED AC 2010; 20:147-51. [DOI: 10.3851/imp1500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Computer-aided drug design has seen constantly increasing application over the past two decades in every area of drug discovery. It can offer significant advantages over conventional approaches, being far less expensive and faster than conventional methods, or offering the possibility to predict molecular behaviours that cannot be elucidated in any other way. Recent developments in software and hardware make it possible to simulate increasingly complex molecular environments, widening the applicability of in silico studies from the interactions of small molecules with key protein residues, to the simulation of the dynamic evolution of complex biological systems with atomic resolution. Antiviral research offers several open challenges, from a biological, biochemical and pharmaceutical point of view. Computational approaches are already providing some answers and will undoubtedly give more in the near future. Here, we present a brief overview of the cutting-edge computational methods that play a major role in present and future antiviral research.
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Affiliation(s)
- Nicola Zonta
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
| | - Antonio Coluccia
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
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Romagnoli R, Baraldi PG, Carrion MD, Cara CL, Cruz-Lopez O, Tolomeo M, Grimaudo S, Di Cristina A, Pipitone MR, Balzarini J, Zonta N, Brancale A, Hamel E. Design, synthesis and structure-activity relationship of 2-(3',4',5'-trimethoxybenzoyl)-benzo[b]furan derivatives as a novel class of inhibitors of tubulin polymerization. Bioorg Med Chem 2009; 17:6862-71. [PMID: 19736015 DOI: 10.1016/j.bmc.2009.08.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 12/01/2022]
Abstract
The biological importance of microtubules in mitosis and cell division makes them an interesting target for the development of anticancer agents. Small molecules such as benzo[b]furans are attractive as inhibitors of tubulin polymerization. Thus, a new class of inhibitors of tubulin polymerization based on the 2-(3',4',5'-trimethoxybenzoyl)-benzo[b]furan molecular skeleton, with electron-donating (Me, OMe or OH) or electron-withdrawing (F, Cl and Br) substituents on the benzene ring, was synthesized and evaluated for antiproliferative activity, inhibition of tubulin polymerization and cell cycle effects. Adding a methyl group at the C-3 position resulted in increased activity. The most promising compound in this series was 2-(3',4',5'-trimethoxybenzoyl)-3-methyl-6-ethoxy-benzo[b]furan, which inhibits cancer cell growth at nanomolar concentrations and interacts strongly with tubulin by binding to the colchicine site.
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Affiliation(s)
- Romeo Romagnoli
- Dipartimento di Scienze Farmaceutiche, Università di Ferrara, Via Fossato di Mortara 17-19, 44100 Ferrara, Italy.
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