Progress Report No. 17

Progress report of the Biomedical Computer Laboratory, covering period 1 July 1980 to 30 June 1981

Progress Report No. 7

Progress report of the Biomedical Computer Laboratory, covering period 1 July 1970 to 30 June 1971

Progress Report No. 4

Progress report of the Biomedical Computer Laboratory, covering period 1 July 1967 to 30 June 1968

Washington University Record, March 19, 2004

https://digitalcommons.wustl.edu/record/1995/thumbnail.jp

Progress Report No. 10

Progress report of the Biomedical Computer Laboratory, covering period 1 July 1973 to 30 June 1974

Intuitive visualization of surface properties of biomolecules

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of colour to encode both characteristics makes the simultaneous visualization almost impossible. This is why most of the times EP and MLP are presented in two different images. In this thesis, we describe a novel and intuitive code for the simultaneous visualization of these properties. For our purpose we use Blender, an open-source, free, cross-platform 3D application used for modelling, animation, gaming and rendering. On the basis of Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins motion with the simultaneous visualization of their chemical and physical features. Blender's Game Engine, equipped with specific physico-chemical rules is used to elaborate the motion of proteins, interpolating between different conformations (NMR collections or different X-rays of the same protein). We obtain a physically plausible sequence of intermediate conformations which are the basis for the subsequent visual elaboration. A new visual code is introduced for MLP visualization: a range of optical features that goes from dull-rough surfaces for the most hydrophilic areas to shiny-smooth surfaces for the most lipophilic ones. This kind of representation permits a photorealistic rendering of the smooth spatial distribution of the values of MLP on the surface of the protein. EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein. Our system permits EP and MLP simultaneous visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Moreover, this representation contributes to gain insight into the molecules function by drawing viewer's attention to the most active regions of the protein

Ethnography of pedagogy and visual cultures in contemporary structural biology

Thesis (Ph. D. in History, Anthropology, and Science, Technology and Society (HASTS))--Massachusetts Institute of Technology, Program in Science, Technology and Society, 2007.Includes bibliographical references (p. 260-277).This ethnography tracks visualization and pedagogy in the burgeoning field of structural biology. Structural biologists are a multidisciplinary group of researchers who produce models and animations of protein molecules using three-dimensional interactive computer graphics. As they ramp up the pace of structure determination, modeling a vast array of proteins, these researchers are shifting life science research agendas from decoding genetic sequence data to interpreting the multidimensional forms of molecular life. One major hurdle they face is training a new generation of scientists to work with multi-dimensional data forms. In this study I document the formation and propagation of tacit knowledge in structural biology laboratories, in classrooms, and at conferences. This research shows that structural biologists-in-training must cultivate a feel for proteins in order to visualize and interpret their activity in cells. I find that protein modeling relies heavily on a set of practices I call the body-work of modeling. These tacit skills include: a) forms of kinesthetic knowledge that structural biologists gain through building and manipulating molecular models, and by using their own bodies as mimetic models to help them figure out how proteins move and interact; and b) narrative strategies that assume a teleological relationship between form and function, and which figure proteins through analogies with familiar human-scale phenomena, such as the pervasive description of proteins as "machines." What I find is that these researchers are not only transforming the objects of life science research: they are training a new generation of life scientists in forms of knowing attuned to the chemical affinities, physical forces and movements of protein molecules, and keyed to the tangible logic and rhetoric of "molecular machines."(cont.) This research builds on concerns in the feminist science studies literature on modes of embodiment in scientific practice, and contributes to studies of performance in science by examining visual cultures as performance cultures. In addition, I incorporate historical studies of the life sciences to map the making of the protein-this intricately crafted entity whose forms and functions, I argue, are recalibrating scientific expertise, reanimating biological imaginations, and reconfiguring the very contours and temporalities of "life itself."by Natasha Myers.Ph.D.in History, Anthropology, and Science, Technology and Society (HAST

Progress Report No. 16

Progress report of the Biomedical Computer Laboratory, covering period 1 July 1979 to 30 June 1980