Biomolecular Visualization Research Articles

Abstract 1094 Validation of Biomolecular Visualization Assessments through Large Scale Field Testing and Student Focus Groups

Abstract 1094 Validation of Biomolecular Visualization Assessments through Large Scale Field Testing and Student Focus Groups

Abstract 1089 A Tale of Two Perspectives: Comparing Student and Faculty Perceptions of Biomolecular Visualization Assessment

Abstract 1089 A Tale of Two Perspectives: Comparing Student and Faculty Perceptions of Biomolecular Visualization Assessment

Seeing Eye to Eye? Comparing Faculty and Student Perceptions of Biomolecular Visualization Assessments

While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular visualization skills. Among these are the lack of consensus about what constitutes competence and limited understanding of student and instructor perceptions of visual literacy tasks. In this study, we administered a set of biomolecular visualization assessments, developed as part of the BioMolViz project, to both students and instructors at multiple institutions and compared their perceptions of task difficulty. We then analyzed our findings using a mixed-methods approach. Quantitative analysis was used to answer the following research questions: (1) Which assessment items exhibit statistically significant disparities or agreements in perceptions of difficulty between instructors and students? (2) Do these perceptions persist when controlling for race/ethnicity and gender? and (3) How does student perception of difficulty relate to performance? Qualitative analysis of open-ended comments was used to identify predominant themes related to visual problem solving. The results show that perceptions of difficulty significantly differ between students and instructors and that students’ performance is a significant predictor of their perception of difficulty. Overall, this study underscores the need to incorporate deliberate instruction in visualization into undergraduate life science curricula to improve student ability in this area. Accordingly, we offer recommendations to promote visual literacy skills in the classroom.

Richard Lerner's Bioinspiration: Biomolecular Visualization and Modeling at Scripps Research

AbstractIn thinking back on Richard Lerner's impact on our lab's trajectory at Scripps Research, we see his fingerprints on all the efforts we have undertaken over the last 40 years. Immunology and virology have been a continuing driving focus in our software development and application within the Molecular Graphics Lab (now the Center for Computational Structural Biology – CCSB), spurred on by the marriage of chemistry with biology that Richard enabled at Scripps. Many of our earliest and continuing computational docking targets have been focused on HIV with collaborations with Chi‐Huey Wong and Barry Sharpless. Along with subsequent computational work with Jeff Kelly, Reza Ghadiri, Udi Keinan and Ben Cravatt we have been able to sustain continuous efforts in developing and applying docking and other computational technologies to structural chemistry problems. In this remembrance, we give our reflections of Richard Lerner's character, vision, and his inspiration in our scientific lives and in the environment that he created at Scripps Research.

Exploring protein symmetry at the RCSB Protein Data Bank.

The symmetry of biological molecules has fascinated structural biologists ever since the structure of hemoglobin was determined. The Protein Data Bank (PDB) archive is the central global archive of three-dimensional (3D), atomic-level structures of biomolecules, providing open access to the results of structural biology research with no limitations on usage. Roughly 40% of the structures in the archive exhibit some type of symmetry, including formal global symmetry, local symmetry, or pseudosymmetry. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (founding member of the Worldwide Protein Data Bank partnership that jointly manages, curates, and disseminates the archive) provides a variety of tools to assist users interested in exploring the symmetry of biological macromolecules. These tools include multiple modalities for searching and browsing the archive, turnkey methods for biomolecular visualization, documentation, and outreach materials for exploring functional biomolecular symmetry.

Identifying Student Misconceptions in Biomolecular Visualization in the Context of the BioMolViz Framework

BioMolViz is a community dedicated to improving visual literacy instruction in biology, chemistry, and biochemistry classrooms. To help instructors approach biomolecular visualization instruction, visual literacy concepts are catalogued through the BioMolViz Framework, which presents overarching themes that are subdivided into learning objectives and goals. A main focus of our project is the creation of open‐access assessments associated with each of the Framework learning goals. Through nationwide workshops held over the past four years, faculty teams wrote and revised assessments to probe students’ visual literacy utilizing the BioMolViz Framework. As part of a pre‐workshop activity, we asked faculty to identify student misconceptions in visualization that they observed in their teaching. These were collected, mapped to the framework, and coded for Bloom's taxonomy level. Frequently mentioned misconceptions of broad relevance to biomolecular visualization skills were mapped to the BioMolViz Framework and formatted into a biomolecular visualization literacy misconception survey. We present the process of survey development and invite educators from any higher education institution to contribute to understanding the prevalence of these misconceptions among student populations by participating in our survey. We hope the survey data will allow the community to develop better pedagogical approaches to biomolecular visualization through awareness of student misunderstandings. Our collective contributions can help our students overcome the most common challenges in biomolecular visualization while improving abilities in this foundational skill set.

Teaching Biomolecular Visualization Literacy: Guidelines for Developing Assessments, Images and Rubrics Aligned with the BioMolViz Framework

Experts in the life sciences glean critical information from biomolecular visualizations. When teaching, we assume our students grasp the concepts in these depictions of biomolecules in the same way that experts do. However, biomolecular visualization (BMV) skills must be intentionally taught and assessed to gauge student understanding. To identify misperceptions and assess comprehension, BioMolViz developed a framework outlining the required skills for biomolecular visualization literacy. Over the past four years, BioMolViz conducted numerous workshops to engage the broader community in creating assessments aligned with the BMV framework, with the goal of developing a repository of validated assessments that can be used by the broader community. Workshops were shifted to an online format during the COVID‐19 pandemic, and a new working group emerged, the BioMolViz Fellows. This subset of workshop participants continued writing and revising assessments remotely, augmenting the group’s peer review and validation process. Our workshops and the ongoing work of the Fellows generated over 200 assessments at various stages in our validation process, with 80 that underwent at least two rounds of revision, and 27 assessments are pending review by an external expert panel. Here, the Fellows present guidelines for generating excellent images using popular visualization software, such as PyMOL, Chimera, and iCn3d. We also provide tips and tricks for designing or reframing questions and rubrics to help instructors maximize student understanding of important biomolecular concepts. Fellows crafted these guidelines using the BMV framework coupled with the lessons learned through workshops.If you are interested in joining our growing community of professionals dedicated to improving BMV instruction, then we’d be delighted to connect with you.

Developing Assessments to Gauge Biomolecular Visual Literacy: A 5 step approach to ensuring accuracy and reliability

BioMolViz is a community of educators, assessment experts, and biomolecular visualization enthusiasts dedicated to improving biomolecular visual literacy. A central goal of the project is to create a repository of validated assessments that instructors can use in their classrooms to gauge students’ visual literacy. Through three‐day workshops, we convene faculty to craft and peer review biomolecular visualization assessments in teams. These workshops are often the first step in our assessment development process. In this presentation, we will describe a five‐step model for designing and validating assessments that consists of: 1. Item creation 2. Item revision 3. Expert panel review 4. Field testing and 5. Dissemination through the online BioMolViz repository. Results from the first three phases of the process will be reported, and our plan for field testing and disseminating assessments will be discussed. In 2020, our workshops and assessment development model moved online, which opened up new pathways for sustained engagement with workshop participants. In particular, we will share how a new working group emerged when we established our remote workflow. A subset of the group, The BioMolViz Fellows, continued working with our community for several semesters and has become integral to the iterative assessment revision process. Alongside our validation process, we will highlight insights for building online communities, establishing remote workflows, and sustaining long‐term participant engagement.

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and molecular interactions. Various programs allow a learner to manipulate 3D structures, and biomolecular modeling promotes active learning, builds computational skills, and bridges the gap between two dimensional textbook images and the three dimensions of life. A critical skill in this area is to model a protein active site, displaying parts of the macromolecule that can interact with a small molecule, or ligand, in a way that shows binding interactions. In this protocol, we describe this process using four freely available macromolecular modeling programs: iCn3D, Jmol/JSmol, PyMOL, and UCSF ChimeraX. This guide is intended for students seeking to learn the basics of a specific program, as well as instructors incorporating biomolecular modeling into their curriculum. The protocol enables the user to model an active site using a specific visualization program, or to sample several of the free programs available. The model chosen for this protocol is human glucokinase, an isoform of the enzyme hexokinase, which catalyzes the first step of glycolysis. The enzyme is bound to one of its substrates, as well as a non-reactive substrate analog, which allows the user to analyze interactions in the catalytic complex.

Modeling an Enzyme Active Site using Molecular Visualization Freeware.

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and molecular interactions. Various programs allow a learner to manipulate 3D structures, and biomolecular modeling promotes active learning, builds computational skills, and bridges the gap between two dimensional textbook images and the three dimensions of life. A critical skill in this area is to model a protein active site, displaying parts of the macromolecule that can interact with a small molecule, or ligand, in a way that shows binding interactions. In this protocol, we describe this process using four freely available macromolecular modeling programs: iCn3D, Jmol/JSmol, PyMOL, and UCSF ChimeraX. This guide is intended for students seeking to learn the basics of a specific program, as well as instructors incorporating biomolecular modeling into their curriculum. The protocol enables the user to model an active site using a specific visualization program, or to sample several of the free programs available. The model chosen for this protocol is human glucokinase, an isoform of the enzyme hexokinase, which catalyzes the first step of glycolysis. The enzyme is bound to one of its substrates, as well as a non-reactive substrate analog, which allows the user to analyze interactions in the catalytic complex.

BioMolViz: A Community Devoted to the Assessment of Biomolecular Visual Literacy

Educators in the molecular life sciences rely heavily on visual representations of biological molecules. The explicit instruction of visual literacy of the representations, however, is frequently overlooked, leaving students confused about what information is being communicated and/or assessed. The BioMolViz learning community was developed to bring attention to the need for visual literacy instruction and assessment distinct from the interpretation of these representations. Over the past several years, BioMolViz has organized interactive workshops devoted to enhancing instructor skillsets through the collaborative development of biomolecular visualization (BMV) assessments. In response to the pandemic, this year the workshops were moved online. In these workshops, participants engage with like minded scientists to design and peer review BMV assessments and share BMV resources, tools, and activities. Using the BioMolViz Framework (biomolviz.org), a tool that unpacks twelve overarching themes of BMV into a collection of learning goals and objectives, participants produce high-quality assessment instruments for evaluating visual literacy skills, which will be made broadly available to the molecular life sciences community through an online repository. We have found that our process encourages collaboration while developing assessment strategies, which has the added benefit of enriching the pedagogy of our growing community of educators. We will present our strategies for creating engaging workshops, the translation of these meetings to effective online experiences, and challenges resulting from the shift to online format. Guided by participant surveys, we have modified the online experience, and will share our plans for future improvements to increase interactivity and sense of community. We invite the members of ASBMB to join our community of practice, providing an opportunity to expand their engagement with our growing and evolving network of collaborating educators.

TactViz: A VMD Plugin for Tactile Visualization of Protein Structures

Scientific disciplines spanning biology, biochemistry, and biophysics involve the study of proteins and their functions. Visualization of protein structures represents a barrier to education and research in these disciplines for students who are blind or visually impaired. Here, we present a software plugin for readily producing variable-height tactile graphics of proteins using the free biomolecular visualization software Visual Molecular Dynamics (VMD) and protein structure data that is publicly available through the Protein Data Bank. Our method also supports interactive tactile visualization of proteins with VMD on electronic refreshable tactile display devices. Employing our method in an academic laboratory has enabled an undergraduate student who is blind to carry out research alongside her sighted peers. By making the study of protein structures accessible to students who are blind or visually impaired, we aim to promote diversity and inclusion in STEM education and research.

Meeting report: BioMolViz workshops for developing assessments of biomolecular visual literacy.

While molecular visualization has been recognized as a threshold concept in biology education, the explicit assessment of students' visual literacy skills is rare. To facilitate the evaluation of this fundamental ability, a series of NSF-IUSE-sponsored workshops brought together a community of faculty engaged in creating instruments to assess students' biomolecular visualization skills. These efforts expanded our earlier work in which we created a rubric describing overarching themes, learning goals, and learning objectives that address student progress toward biomolecular visual literacy. Here, the BioMolViz Steering Committee (BioMolViz.org) documents the results of those workshops and uses social network analysis to examine the growth of a community of practice. We also share many of the lessons we learned as our workshops evolved, as they may be instructive to other members of the scientific community as they organize workshops of their own.

Building a Community of Practice for the Assessment of Biomolecular Visual Literacy

The ability to understand, interpret, and create molecular images is a critical learning objective in biochemistry and molecular biology courses. Yet biomolecular visualization skills are rarely explicitly taught. Over a two‐year period, the BioMolViz group organized seven one‐day workshops to explore and establish best practices for the generation, revision, and finalization of biomolecular visualization (BMV) assessments. Our process utilizes a BMV framework (biomolviz.org) to build targeted assessments that address specific learning goals and objectives. We then revise the assessments through a peer review process and integrate a final analysis of images for accessibility to those who are colorblind. Although there is a wealth of information to guide the creation of multiple‐choice questions, we have found that there are few resources for the generation and evaluation of other types of assessments. For example, BMV assessments are more likely to be open‐ended and specifically target molecular visualization skills (e.g. require the student to create an image of DNA or identify a structural feature on a given image of a protein). We invite participants to help us address this gap and refine our method for generating assessments by attending our upcoming three‐day NSF‐funded summer workshops. Activities will include revising existing assessments and creating instruments of interest to new participants. In addition to producing high‐quality BMV assessments aligned with the framework, these workshops will offer a unique professional development for instructors interested in promoting visual literacy by building a community of practice for the instruction of BMV skills.Support or Funding InformationThis work was supported by the National Science Foundation under award numbers DUE‐1022793, ‐1323414, ‐1503811, IUSE‐1712268, and RCN‐UBE‐1920270. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models.

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure-function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure-function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA supercoiling dynamics. We also designed accompanying assessments to gauge student learning. Students responded favorably to the modules and showed normalized learning gains of 49% with respect to their ability to understand and relate molecular structures to biochemical functions. By incorporating accurate 3D printed structures, these modules represent a novel advance in instructional design for biomolecular visualization. We provide instructors with the materials necessary to incorporate each module in the classroom, including instructions for acquiring and distributing the models, activities, and assessments. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):303-317, 2019.

A Competency‐Based Approach to Developing Biomolecular Visual Literacy

When you show a visual representation of a biomolecule, do your students “see” what you “see”? Are they able to interpret the model correctly and draw appropriate conclusions about the structure and atomic/molecular interactions? Do they grasp that cartoon and space‐filling models represent the same protein? Biochemistry instructors use visual representations of biomolecules to teach many concepts, yet there are few tools and frameworks to assess whether students can interpret these models. The BioMolViz.org group is a team of educators developing these tools. Over four years, we have identified a set of overarching themes that encompass biomolecular visualization skills with teachable objectives. We define proficiency levels for the objectives, describe student competency within the objective at the novice (first year) and amateur (junior/senior year) levels, and link these competencies with assessment questions. For example, the objective: “students will describe the significance of the monomer unit location within the three‐dimensional structure of a polymer” can be applied throughout the student's academic career. Novice students would be expected to identify the termini of a biological polymer, while more advanced students would catalog interactions of monomers that stabilize the macromolecule. Here, we present our current efforts on this Biomolecular Visualization Framework, including the results from four National Science Foundation‐funded 2018 workshops and our diversity SACNAS/ABRCMS outreach efforts. We propose targeted visual literacy development will enable students to understand the structure and associated function of biomolecules. The BioMolViz.org website makes resources widely available to help instructors facilitate this growth.Support or Funding InformationThis work was supported by the National Science Foundation under award numbers DUE‐1022793, ‐1323414, ‐1503811 and IUSE‐1712268. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Visualizing Biochemistry: The Implementation of Biomolecular Visualization and Structure‐Function Conceptual Game‐based Card Sorting Activities

Biochemistry, at the undergraduate level, is in a distinctive position to unveil misconceptions as the topics covered are abstract and require recollection of content from prior STEM courses. These components, when compounded with myriad of representations, likely exceed the cognitive load of the students and therefore propagate misconceptions. Current research suggests that undergraduate students learn visual literacy skills indiscriminately throughout his/her academic career. Therefore, we propose that direct instruction of biomolecular visualization will reduce the cognitive load and increase conceptual understanding.This study aims to answer the questions: Do targeted interventions improve accuracy and precision of card sorting across the semester? and Do targeted interventions increase conceptual understanding of structure and function across the semester? Preliminary findings from pre‐ and post‐ “free sort” card sorting activities in control semesters provided evidence for the design of a series of interventions. These interventions aim to increase the visual literacy of undergraduate biochemistry students while simultaneously increasing structure‐function content understanding using game‐based card sorting activities. Game‐based learning is used to increase motivation, comprehension, and sense of achievement in students. Three interventions were designed and implemented into the biochemistry curriculum for fall 2017. Student responses from these activities and the matching card section on exams were analyzed in addition to the pre‐ and post‐”free sort” card sorting activities. These data are compared to control groups from two previous semesters. Furthermore, the data are analyzed using qualitative inferential, quantitative inferential, and descriptive statistical analysis. Refinement of the interventions will continue into future semesters of biochemistry with the intention of setting a standard of targeted instruction of visual literacy skills.Support or Funding InformationThis project is partially supported by the National Science Foundation under award number DUE1323414 to Milwaukee School of Engineering.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Assessment of Visual Literacy Skill Gains in Graduate Biochemistry

Biochemistry II, a culminating course of the biochemistry master's degree program at the University of Saint Joseph, emphasizes protein structure, folding, catalysis, and mechanism. Accordingly, the course has a significant molecular modeling component. Students are taught to render and manipulate proteins in PyMOL through tutorials that span the basics of the program, measurement and evaluation of potential molecular interactions, assessment of mutations, and prediction of protein function based on structural features. To evaluate students' progress in their ability to interpret visual representations of macromolecules, we designed a study using several of the overarching visual literacy themes outlined by the BioMolViz group (BioMolViz.org). At the beginning of the course, students complete a pretest in which they view macromolecule structures and answer questions that encompass several of the overarching visual literacy themes to evaluate their baseline biomolecular visualization skills. At the end of the semester, students complete an exit evaluation, which contains unique questions that mirror the first assignment. Students demonstrated improvement in each of the visual literacy themes evaluated, with the most significant gains in the structure‐function relationship and structural model skepticism areas. Here, we present the results of the assessment from three unique sections of the course, along with an overview of the tutorials and assignments being used to build visual literacy skills. Likewise, we will discuss revised course materials addressing areas in which students did not initially achieve the expected gains.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

ESES: Software for Eulerian solvent excluded surface

Solvent excluded surface (SES) is one of the most popular surface definitions in biophysics and molecular biology. In addition to its usage in biomolecular visualization, it has been widely used in implicit solvent models, in which SES is usually immersed in a Cartesian mesh. Therefore, it is important to construct SESs in the Eulerian representation for biophysical modeling and computation. This work describes a software package called Eulerian solvent excluded surface (ESES) for the generation of accurate SESs in Cartesian grids. ESES offers the description of the solvent and solute domains by specifying all the intersection points between the SES and the Cartesian grid lines. Additionally, the interface normal at each intersection point is evaluated. Furthermore, for a given biomolecule, the ESES software not only provides the whole surface area, but also partitions the surface area according to atomic types. Homology theory is utilized to detect topological features, such as loops and cavities, on the complex formed by the SES. The sizes of loops and cavities are measured based on persistent homology with an evolutionary partial differential equation-based filtration. ESES is extensively validated by surface visualization, electrostatic solvation free energy computation, surface area and volume calculations, and loop and cavity detection and their size estimation. We used the Amber PBSA test set in our electrostatic solvation energy, area, and volume validations. Our results are either calibrated by analytical values or compared with those from the MSMS software. © 2017 Wiley Periodicals, Inc.

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies.

A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three‐dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure‐function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69–75, 2017.