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MolTour: a biochemistry VR explorer

Matthias Debernardini
Kristina Sen
Emylie Nguyen


MolTour is a website that classrooms can use to explain molecules to students more easily. It allows students and teachers to explore proteins in virtual or augmented reality. Presentations can be made ahead of time to create a tour of a molecule. The students then access the website from their mobile browsers and then they slide their phones into their google cardboards. Students in a lecture can then work together. This allows students to better understand the relationship between chemical properties and physical structure. This can allow the students to greatly understand their studies better.


Why does the traditional educational system need reforms? Educational institutions provide us with instrumentally valuable information and ‘initiate’ us into different communities by shaping our values and influencing our interests (Peters, 1970). We all agree that information becomes irrelevant over time, values constructed by communities are prone to change as well, in other words, the content of education is changing. Should this change extend to ways of providing students with educational content?

In the middle of the 20th century Hannah Arendt argued that we should preserve the traditional system of education (Arendt, 2006). Active change of it, based on our predictions of what future students might need, deprives them of the ability to make their own choices, and thus dampens the real innovation. Put more intuitively, our expectations shape not only our future but the future of the generations to come. New students will enter the educational system created by us, and this system will help them acquire and sharpen the skills that we will have defined for them.

As time passed, however, not only the content of traditional education has changed. The emergence of educational studies and piqued interest in education from other scientific fields undermined Arendt’s argument in two ways. First of all, views on the educational system, being a subject of studies and educational content in itself, are prone to change. Secondly, better learning and understanding of the material is achieved if the educational format is content-dependent.

In many fields of study, in biochemistry, in particular, understanding of the subject depends on the understanding of abstract concepts within this subject. For example, the properties of the substances are determined by the structures of the molecules. Understanding such structures is vital, and is very difficult to achieve with 2D pictures (Libman & Huang, 2013). Neuroscientific research has shown that increased imageability of the learning material significantly contracts the difference in outcomes of learning of abstract and concrete concepts (Binkofski & Borghi, 2014).

The use of molecular viewer apps has been proven to be effective at simulating the 3D imageability of the molecules (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014). Interactive learning stimulates the student engagement and refreshes the concentration span of students during the lessons (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014). If students are provided with clear instructions, and the responsible behavior is promoted by the teachers (Williams & Pence, 2011), the use of technology enhances the learning experience and increases concentration.

Keeping in mind the goals of education, set out as the transfer of instrumental information and non-instrumental interests and values, active change of the educational system should not scare us. We should want to reform education, as new and more effective ways of sparking interest and transferring knowledge are found. We are presenting one such way, aiming at introducing the use of VR among biochemistry students to study the structure of molecules.

Status quo

Deep understanding of properties of different substances is expected from the biochemistry students. As properties of the substances are determined by the structures of molecules, students need to have an accurate representation of the structures as well. It is impossible to achieve an accurate imageability of complicated structures through the 2D image, and physical models are impractical and not always available. Thus, we propose using technology to achieve accurate imageability, and the use of the app, in the creation of which we participated, in particular.

Another issue arising during the lessons is an inefficient use of time. When explaining certain materials lecturers would often show images of molecules on the screen. The amount of time needed for such an explanation could bring better results if students could explore the structures of the molecules themselves. It is up to the teachers whether to let students interact with the app in class to refresh the concentration span of the students, or to assign them to use the app at home and to spend their time in a classroom differently.

We believe that the use of technology in classrooms can enhance the transmission of information, match the interests of students and spark the interest in the subject of studies. In the particular case of biochemistry students, the use of the MolTour app can increase the learning results by providing students with accurate imageability of the molecules. The interactive element can increase the student engagement, and the usage of the app can be seen as a small break during the lecture, which will allow for better concentration afterward.

Philosophical perspective

In the field of philosophy of education, there have been different opinions on whether we should move away from the traditional system of education. One of the critiques of the project of rebuilding education was raised by Hannah Arendt in the middle of the last century. In her essay ‘The Crisis of Education’ (1954) she elaborates on the concepts of natality, innovation, and the progress for the world.

Arendt states that ‘the essence of education is natality, the fact that human beings are born into the world’. As new human beings are born, in each of them there is a hope for progress and renewal. If the world is not renewed, our future lies in regress and ruin. In every newborn person, there is a hope for a new beginning and a potential action. However, newcomers into the world are late comers as well: they enter a pre-existing system of which we are the representatives.

According to Arendt, it is our moral duty to represent the world as it is, and not try to prepare students for the future, as we predict it to be. Our expectations will define the future for us, and for the generations to come, and in this manner, the real innovation will never come, as everything is predetermined by people already existing in the system.

An answer to Arendt’s critique might be found in the views of another prominent philosopher, specializing in education in particular. Richard Peters argued that education itself cannot be possible without us influencing students entering the system (1970). Education is a process of transferring values, views and interests to the same, if not to the larger degree as of transmitting instrumental information. Education is always ‘initiation’ of newcomers into a certain community sharing views, beliefs, and values.

Those views, beliefs, and values, being socially constructed are prone to change. With the passage of time, we find some studies more valuable than others, we change our views on the main findings within sciences, there are observable shifts of scientific and academic interests. The world around us is changing, and those changes are inevitably reflected in the process of transmitting values and interests from educators to students, even if the educational system stays fixed.

Thus, we believe that keeping the educational system unchanged only leads to inefficiencies in transferring information and in transmitting values and sparking interests. Neuroscientific and technological perspectives show that more effective ways of educating in Peters’ sense have been found. Keeping the goals of education in mind, which are the transfer of information as well as values and interests, we argue that educational system should be made more effective and efficient, and technology is one of the ways of doing so.

Neuroscientific perspective

Conventionally, when describing learning material, we refer to concepts as being concrete or abstract (Paivio, 1991) (Schwanenflugel, 1988) (Desai, 2010). There is no standard way of drawing this distinction, but for human beings, there is an intuitive difference between concepts like chairs or tables, and concepts like happiness or freedom. We systematically show better understanding and learning of concrete concepts over the abstract ones (Binkofski & Borghi, 2014), but the hypotheses about the mechanisms underlying such processes are fairly recent and still contested.

According to the classical dual-coding hypothesis in neuroscience, there is a certain concreteness effect explaining better understanding and memorization of concrete objects. As we ultimately rely on words in our understanding, the verbal system is involved in the learning of both types of concepts. We usually learn concrete concepts by interacting with them and seeing them in relation to other concrete concepts, so our visual system is in work (Paivio, 1991). The better understanding of concrete concepts is due to the additional system of processing information that is involved.

The context availability theory suggests that concrete concepts are situated in a richer context overall, more related to our semantic knowledge which again leads to better understanding and memorization (Schwanenflugel, 1988). New research has found, however, that if we control for the imageability, which is a variable related to the learning material and not to the systems of processing information, differences in learning and understanding of the concrete and abstract concepts decrease (Binkofski & Borghi, 2014).

As properties of the substances are determined by the structure of their molecules, understanding of such structures is required for biochemistry students. It is impossible to achieve accurate imageability of the molecules through pictures (Libman & Huang, 2013), and physical models are impractical and not always accessible. Redesign that we propose aims at increasing the accurate imageability of molecular structures in 3D, which will enhance biochemistry students’ understanding and memorization of the material.

Technological perspective

Traditional lectures are not the most efficient way of teaching Biochemistry and can be improved upon in many ways. Firstly, having a one-way knowledge transfer does not increase student engagement and active participation. Besides, students have an average concentration span of 20 minutes only (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014). Secondly, some students lack the ability to mentally manipulate two-dimensional structures and to convert them to three-dimensional structures. These difficulties can be overcome by using technology to augment education. Smartphones are popular among college students and instead of viewing this increased use as a problem, it should be regarded as an opportunity to engage large groups of students. Furthermore, smartphones can be powerful tools to enhance the understanding of abstract concepts(Wijtmans, van Rens & van Muijlwijk-Koezen, 2014), provided that the teacher guides the students through this process. This means that no matter how the teacher wishes to incorporate technology in class, e.g. devoting a total of ten minutes of class to 3D visualization tasks, the teacher is still responsible for providing students with clear instructions to manage attention (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014), (Williams & Pence, 2011).

3D visualization apps

Molecular viewer apps (or software) for mobile devices are powerful tools to simulate ‘3D’ feeling for molecular systems (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014). These apps often allow students to switch between different viewing modes of the molecule (space-filling model or ball and stick model). Furthermore, the student is able to rotate as well as zoom in on the molecule. Additional information such as the type of atom and bond length is given after clicking on specific parts of the molecule. Structures of small molecules can be downloaded from databases such as PubChem and large biomolecules such as proteins from the PDB database (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014), (Libman & Huang, 2013). This allows the students to explore the binding site of proteins and to understand the interactions between small molecules and proteins. Understanding these interactions is essential in Biochemistry and especially in drug-discovery research but these relationships are not always represented well enough using two-dimensional representations in textbooks or slides (Libman & Huang, 2013). Students should ‘see’ it for themselves and that is exactly why molecular viewer apps should be used more often during class to enhance understanding of the material. This interactive learning stimulates student engagement. However, since smartphones are used for 3D visualization of molecules, responsible behavior of students is required with respect to possible distractions such as social media, games, etc (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014). Furthermore, the teacher is also responsible for the provision of clear instructions. The teacher could, for instance, let students explore the molecule for a couple of minutes after having provided some background information about the molecule itself. In addition, worksheets could be given to students which contain problems that can only be solved with the help of 3D visualization apps. These interactive tasks refresh the concentration span and are a good way to assess student understanding of the material and concepts (Wijtmans, van Rens & van Muijlwijk-Koezen, 2014).


The MolTour website – click here

We present MolTour, an online platform for educators to prepare VR/AR presentations of molecules. The app works by requesting data files from PDB or other protein data banks and using the integrated 3D engine displays the molecules in 3D. Many 3D visualizations apps already exist, however they exist purely as standalone apps – meaning that the underlying operating system needs to be compatible. This app purely hosted by the browser, which removes the compatibility and permissions needed to run software natively. In addition, there are many devices that support the latest browsers, this include laptops and smartphones. A lecturer can easily integrate this into their classroom by deciding which molecules they would like and then choosing how to display them. Various rendering modes are supported by the underlying 3D engine. In addition, viewpoints can be selected ahead of time and cycled through, for instance showing the underside to reveal a bond not seen from the front side. Bonds and Atoms can be displayed using different colors and more than one molecule can be shown at the time. The application enters VR mode by selecting VR mode in the website and sliding the phone device into a compatible VR headset (many affordable and high end models exist). The app connects to the accelerometer of the phone and translate head rotation to camera rotation, which in turn changes the relative orientation of the molecule presented to the user. Teachers and students can connect to the same networked session, meaning that the teacher can control the view of the students and tour them around points of interest. Efforts are currently under way to present the molecule using AR technology as well, which would remove the need for a headset. These efforts are also directed towards a graphical WYSIWYG (what you see is what you get) editor.

Guidelines for teachers

The most straightforward to use MolTour is to have it complement a pre existing curriculum. This application does not aim to replace the classroom but to aid lecturers in how they present the material. An effective method is to use the application when explaining the properties of a molecule to a student. These properties are often dependant on the geometry of the molecule which is difficult to convey using words and static 2D images. It is important to let students know that they will be using this platform ahead of time, so that they can charge their phones and get in the right mindset. Another effective use of the application is to hand out a worksheet with questions that have to be answered by understanding the molecule. In this case, the students can group up and show each other interesting parts of the molecule as they explore it together. Thinking about the questions and using the app to answer them can give the students a good understanding and good experience for what it’s like to be able to reason about molecules.


It is difficult for educators in Biochemistry to impart an understanding of the relationships between structure and function of molecules using two-dimensional representations (Berry & Baker, 2010). For this reason, our redesign aims at enhancing student understanding and memorization of the material by using technology to augment education. Students can acquaint themselves and interact with three-dimensional molecules and proteins with the help of 3D visualization apps. This interactive learning stimulates student
engagement and refreshes the concentration span. The implementation of three-dimensional representations is not only confined to Biochemistry and can be extended to other curricula, such as astronomy (Farah & Maybury, 2009) and dental education (Litvak, Yair, 2001), as well.

Student Testimonials

“What did you think about the 3D assignments in the tutorials?”

  • “You could gain more insight into the molecules and the questions fit the material.”
  • “What I liked most was that I could gain an insight into how structures actually look instead of a simplified representation in textbooks.”
  • “You could really explore the molecular structures because of the 3D assignments.”
  • “It is refreshing to not look at an illustration for once.”
  • “You gained an insight into what proteins looked like.”
  • “You could improve spatial reasoning.”
  • “It was interesting to see proteins in 3D.”
  • “I liked how you could see the interactions between enzymes and small molecules.”
  • “Better representation of binding/interactions between molecules compared to images in textbooks.”
  • “The 3D assignments made me understand the material more.”
  • “You were able to recognize important features/characteristics of the molecules.”
  • “They gave a good impression of the material.”


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