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2013 Hanson Prilusky Ijc X.Pdf Review DOI: 10.1002/ijch.201300024 JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia Robert M. Hanson,[a] Jaime Prilusky,[b] Zhou Renjian,[c] Takanori Nakane,[d] and Joel L. Sussman*[e] Abstract: Although Java does not run on some handheld de- forwardly transformed directly into JavaScript, requiring no vices, e.g., iPads and iPhones, JavaScript does. The develop- Java applet, and producing identical graphical results. JSmol ment of JSmol, a JavaScript-only version of Jmol, is de- is thus the first full-featured molecular viewer, and the first scribed, and its use in Proteopedia is demonstrated. A key ever viewer for proteins, which can be utilized with an inter- aspect of JSmol is that it includes the full implementation of net browser on handheld devices lacking Java. Since the Me- the entire set of Jmol functionalities, including file reading diaWiki features of Proteopedia have been modified to op- and writing, scripting, and rendering. The relative perform- tionally use JSmol, the wealth of crowd-sourced content in ances of Java-based Jmol and JavaScript-only JSmol are dis- Proteopedia is now directly available on such devices, with- cussed. We can now confirm that the guiding principles of out the need to download any additional applet. Java programming can be completely and relatively straight- Keywords: bioinformatics · databases · Java · JavaScript · Proteopedia Communicating Science Widely There is a great need to improve the communication of [a] R. M. Hanson+ scientific concepts at all levels, so as to generate a passion St. Olaf College for science in the next generation, as well as to increase Dept. of Chemistry the public understanding of science. Proteopedia[1–3] was Northfield, MN 55057 (USA) developed to tackle this issue via a novel approach. The [b] J. Prilusky+ novelty of Proteopedia lies in the implementation of Bioinformatics Unit a wiki web resource that presents information on the 3D Biological Services structure and function of biological macromolecules Weizmann Institute of Science (Figure 1) as a way of showing the principles of structural Rehovot 76100 (Israel) biology to a broad audience. This includes a wide range [c] Z. Renjian of web users, from high school students to medical school Room 202, Building 38 Nianjiabang Road 425 students, from educators looking for a way to engage Zhoupu Town, Pudong District their students in molecular structure to scientists doing Shanghai 201318 (China) basic and applied research, as well as the general public. [d] T. Nakane Structural biology is concerned with accumulating Dept. of Cell Biology structural information at the atomic level for proteins, nu- Graduate School of Medicine cleic acids, and other biological macromolecules. Such de- Kyoto University tailed information can then be utilized to understand how Yoshidakonoe-cho, Sakyo-ku these macromolecules function, and how they recognize Kyoto 606-8501 (Japan) other molecules with which they interact. However, bio- [e] J. L. Sussman logical macromolecules contain many thousands of atoms Dept. of Structural Biology and the Israel Structural Proteomics Center and, even when displayed on a computer screen as high- Weizmann Institute of Science quality 3D representations, are often very difficult to Rehovot 76100 (Israel) fathom, even for a trained biochemist, let alone for a clini- phone +972-8-934-4531 cian, a layman, or a high school student. fax: +972-8-934-6312 Proteopedia was constructed with the specific objective e-mail: [email protected] of providing a user-friendly tool that would enable under- [+] R. M. H. and J. P. made equal contribution to this paper. Isr. J. Chem. 2013, 53, 207 – 216 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 207 Review J. L. Sussman et al. Robert Hanson is the Edolph A. Larson graduates, graduate students, scientists, and clinical inves- and Truman E. Anderson Sr. Chair of tigators, amongst others, to understand such complex Chemistry and currently serves as chair macromolecular structures and how they function as mi- of the St. Olaf College Chemistry Dept. croscopic bio-nano machines. It has not escaped our He joined the St. Olaf faculty in 1986 notice that the development of such a tool for structural after earning a B. S. from Caltech, biology might serve as a paradigm for developing similar a PhD from Columbia University, and tools for other disciplines, such as astronomy, neuroanato- completing postdoctoral work at MIT. my, architecture, and paleontology. Over the course of his career, Hanson Structural biology has played a cutting edge role in the has been the recipient of many awards immense progress of life science research over the past 60 and grants from organizations that in- clude the NSF, NIH, the ACS, DuPont, years. There have been more than a dozen Nobel Prizes Eli Lilly, and the W. M. Keck Founda- in structural biology since the early 1950s, when Watson [4] tion. Hanson has published numerous articles in the areas of and Crick determined the 3D structure of the DNA chemistry, material science, informatics, and mathematics, as well double helix (Figure 2a). Understanding the basic mecha- as two books: Molecular Origami: Precision Scale Models from Paper nisms of how protein and nucleic acid molecules function and Introduction to Molecular Thermodynamics. He is the co-inventor is crucial for biology. For example, without structural in- on one patent titled Catalytic Asymmetric Epoxidation (with K. Barry sight (Figure 2b), it is impossible to comprehend how the Sharpless, who received the Nobel Prize in Chemistry in 2001). ribosome (the nano-machine that synthesizes all proteins Since 2006 Hanson has been the project leader and principal devel- oper for the Jmol Molecular Visualization Project, a global open- source interdisciplinary effort to develop novel web-based capabili- ties for the visualization of molecular structure and energetics. Ap- Zhou Renjian earned his B. S. in Math- plicable in a wide range of fields, the Jmol applet can be found on ematics at Shanghai Jiao Tong Univer- thousands of websites, including the PDB and Proteopedia. In 2010 sity. He worked as a software engineer Jmol became part of an exhibit on nanotechnology in the Innoven- for IDSignet, Primeton, and Koretide, tions pavilion at the Walt Disney Epcot theme park, where more doing research and development in than 300,000 visitors have interacted with it. He also developed the digital signatures, enterprise software Interim course Medicinal Chemistry in Jamaica: An International platforms, and computer operating sys- Perspective, which brings students to the University of the West tems. He created the open source proj- Indies in Kingston, Jamaica, every other year for an in-depth look ect Java2Script, providing an Eclipse into how drugs work and how they are designed and developed, plugin for converting existing Java code with a particular focus on the interactions of culture, traditional into JavaScript. He also developed and healing, and pharmaceutical medicine. Prof. Hanson may be operated WeBuzz.IM service, providing reached at [email protected]. web messengers for users to connect with their friends on popular instant messaging networks, such as Gtalk, MSN, YMSG, and AIM. Recently, he co-founded Coco Voice with Guo Lei, an app for iOS and Android devices, helping people Jaime Prilusky is the Head of the Bioin- to send text, voice, and pictures to their friends. Mr. Renjian may be formatics Unit at the Weizmann Insti- reached at [email protected]. tute of Science in Rehovot, Israel. He received his PhD in neuroendocrinolo- Takanori Nakane graduated from Kyoto gy from the National University of Cor- University’s School of Medicine in doba, Argentina in 1974, and was a full 2010. After passing Japan’s national professor at the National Technological board exam and qualifying as a medical University in Argentina before joining doctor, Nakane decided to enter a four- the Weizmann Institute in 1989. An year PhD course in X-ray crystallogra- early online pioneer in bioinformatics, phy at Kyoto University instead of clini- Jaime developed the first web interface cal practice. While working on “wet” to search and retrieve PDB data, called experiments, he realized that he is 3DB, and founded BioMOO (a virtual more attracted to “dry” (computation- meeting place for biologists). In addition to Proteopedia his proj- al) aspects of science. Over the last ects include OCA (oca.weizmann.ac.il), a browser-database for pro- two years, Nakane has been developing tein structure/function and GeneCards (www.genecards.org), an molecular viewers for web browsers electronic encyclopedia integrating information about the functions and mobile devices, including the NDKMol molecular viewer that of human genes and their products, and of biomedical applications has been incorporated with the RCSB PDB Mobile app. Nakane based on this knowledge. For more, see http://miw.weizmann.ac.il. also contributes to several open-source projects, including PyMOL Most recently he, together with Joel Sussman & Eran Hodis, has de- and Jmol. Visit http://webglmol.sourceforge.jp to download Na- veloped Proteopedia, the free, collaborative 3D encyclopedia of pro- kane’s GLmol (Molecular viewer on WebGL/Javascript) and ESmol teins & other molecules (http://proteopedia.org). Prof. Prilusky may & NDKmol (Molecular viewer for Android). Dr. Nakane may be be reached at [email protected]. reached at [email protected]. 208 www.ijc.wiley-vch.de
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