Framework

Each section title represents one of the 12 overarching themes of the Biomolecular Visualization Framework. Expand each theme for a list of the learning goals. Expand each goal for a list of the learning objectives. Please cite Dries et al. BAMBED (2017). An earlier online version of the 2017 Framework was formatted as columns.
Download complete 2020 Framework as PDF document.
Download complete 2017 Framework as PDF document.

ß-D-glucose is shown with a “non ideal” bond angle marked in magenta, and the dihedral angle for the C1-C2 bond (carbohydrate numbering) is shown in cyan.Three‐atom and four‐atom (dihedral) angles, metal size and metal‐ligand geometries, steric clashes.

AG1.01 Students can identify atomic geometry/hybridization for a given atom. (Novice)

AG1.02 Students can measure bond angles for a given atom. (Novice)

AG1.03 Students can identify deviations from the ideal bond angles. (Amateur)

AG1.04 Students can explain deviations from the ideal bond angles due to local effects. (Amateur, Expert)

AG1.05 Students can predict the effect of deviations from ideal bond angles on the structure and function of a macromolecule. (Expert)

AG1.06 Students can identify the structural features of a peptide bond. (Novice, Amateur)

AG2.01 Students can describe different conformations that a cyclic structure can adopt using visualization tools. (Amateur)

AG2.02 Students can describe different conformations of atoms about a bond using visualization tools. (Novice)

AG2.03 Students can distinguish energetically favorable and unfavorable conformations that a structure can adopt. (Amateur)

AG2.04 Students can predict the effect of a given conformation on the structure and function of a macromolecule. (Expert)

AG3.01 Students can identify a dihedral/torsion angle in a three-dimensional representation of a macromolecule. (Novice)

AG3.02 Students can identify the planes between which a dihedral/torsion angle exists within a three-dimensional representation of a macromolecule. (Novice)

AG3.03 Students can identify phi, psi, and omega torsion/dihedral angles in a three dimensional representation of a macromolecule. (Amateur)

An alpha helix of the protein lysin (PDB ID: 1lis) rendered 3 ways as cartoon, cartoon + line, and space filling, respectively from left to right.Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

AR1.01 Students can manipulate rendered structures in 3D space. (Novice)

AR1.02 Students can align rendered structures in 3D space. (Amateur)

AR1.03 Students can annotate the differences between multiple aligned structures. (Expert)

AR1.04 Students can infer information from rendering a structure in different ways. (Novice, Amateur, Expert)

AR1.05 Students can create renderings that distinguish secondary structural features. (Novice)

AR1.06 Students can create an information rich rendering of a structure that depicts structural features found in the literature. (Amateur)

AR1.07 Students can create an information rich rendering of a structure containing ligands, covalent modifications, and noncanonical amino acids or nucleotides. (Expert)

AR1.08 Students can use molecular visualization to tell a story about a macromolecular structure. (Expert)

AR1.09 Given the rendering of a macromolecule, students can find hydrogen bonds, ionic bonds and van der Waals contacts in the structure. (Expert)

AR1.10 Students can convert textbook images of small molecules into 3D representations in a molecular visualization program. (Amateur)

AR2.01 Students can recognize that a cartoon rendering is a summary of the detail in a line rendering. (Novice, Amateur)

AR2.02 Students can describe the atoms that are represented in different renderings. (Novice)

AR2.03 Students can identify the best rendering for a specific purpose. (Novice, Amateur)

AR2.04 Students can identify the limitations in various renderings of molecular structures. (Amateur)

AR2.05 Students can understand the level of detail of different molecular representations. (Novice, Amateur, Expert)

AR2.06 Students can transition comfortably between equivalent 2D and 3D renderings of biomolecules. (Novice, Amateur, Expert)

AR2.07 Students can interpret the meaning of color in context. (Novice)

[xxTODO]Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

CA1.01 Students can construct a model of a protein with a ligand. (Novice)

CA1.02 Students can construct a model of a protein with a ligand and identify the types of molecular interactions. (Amateur)

CA1.03 Students can construct a model of a macromolecule bound to a ligand and assess the importance of molecular interactions. (Expert)

CA1.04 Students can produce a model of a biomolecule based on a known structure of a related biomolecule. (Amateur, Expert)

CA2.01 Students can design a rendering that conveys the cellular location or function of a macromolecule based on position of polar and nonpolar functional groups. (Amateur)

CA2.02 Students can explore protein images with colored polar/nonpolar residues to determine whether they fold with a hydrophobic core. (Novice)

CA2.03 Students can create images to display polar/nonpolar residues and propose a role for the protein and/or how it interactions with its environment ‐ and that the predictions would be plausible based on the protein. (Amateur)

CA2.04 Students can make accurate predictions of the location/function of the protein that incorporates additional protein features, such as transmembrane helices, apparent docking surfaces, etc. (Expert)

Deoxymyoglobin (PDB ID: 1a6n) bound to the HEME ligands, and complexed with an iron cofactor (a type of metal cluster).Metals and metal clusters, posttranslational additions such as glycosylation, phosphorylation, lipid attachment, etc.

Note that this theme was formerly called Hetero Group Recognition (HG).

LM1.01 Students can use the annotation associated with a pdb file to identify and locate ligands and modified building blocks in a given biomolecule. (Amateur)

LM1.02 Students can visually identify non‐protein chemical components in a given rendered structure. (Amateur)

LM1.03 Students can distinguish between nucleic acid and ligands (e.g. metal ions) in a given nucleic acid superstructure. (Amateur)

LM1.04 Students can explain how a ligand in a given rendered structure associates with the biomolecule (i.e., covalent interaction with residue X). (Amateur)

LM1.05 Students can explain and demonstrate how ligands and modified building blocks are identified in unannotated structures. (Expert)

LM2.01 Students can look at a given rendered structure and describe how the presence of a specific heterogeneous group alters the structure of that biomolecule. (Amateur)

LM2.02 Students can explain how the removal of a particular ligand or modified building block would alter the structure of a given biomolecule. (Expert)

LM2.03 Students can explain how a specified ligand or modified building block contributes to the function of a given protein. (Amateur)

LM2.04 Students can predict how a ligand or modified building block contributes to the function of a protein for which the structure has been newly solved. (Expert)

A peripheral membrane protein (matrix metalloproteinase) is shown complexed to a lipid bilayer (PDB ID: 2mlr).Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

MA1.01 Students can identify individual structures in a macromolecular assembly. (Novice, Amateur, Expert)

MA1.02 Students can describe functions of individual structures within a macromolecular assembly. (Novice, Amateur, Expert)

MA1.03 Students recognize the various lipid ultrastructures (micelles, bicelles, vesicles, and lipid bilayers) in a 3D structure. (Novice)

MA2.01 Students can render a macromolecular assembly to highlight individual structures. (Amateur)

MA2.02 Students can render a macromolecular assembly to illustrate structural features. (Amateur, Expert)

The NMR structure of the dimeric C-terminal domain of HIV-1 capsid protein (PDB ID: 2kod) shows the dynamics, particularly of the loop regions of the protein, shown in green.Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)

MD1.02 Students can correlate molecular movement with function. (Novice, Amateur, Expert)

MD2.01 Students can locate potential regions of flexibility and inflexibility in the structure of a biomolecule. (Novice, Amateur)

MD2.02 Students can recognize acceptable/unacceptable movement within a macromolecule by determining whether the movement is within allowable bond angles. (Expert)

MD2.03 Students can recognize acceptable/unacceptable movement within a macromolecule by determining whether the movement results in steric hindrance. (Amateur)

MD2.04 Students can recognize acceptable/unacceptable movement within a macromolecule by considering the atomic packing constraints. (Expert)

The lambda repressor (PDB ID: 1lmb) is shown bound to the operator regions of bacterial DNA.Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

MI1.01 Students can distinguish between covalent and noncovalent interactions. (Novice)

MI1.02 Students can identify the different non‐covalent interactions given a 3D structure. (Amateur)

MI1.03 Students can predict whether a functional group (region) would be a hydrogen bond donor or acceptor. (Amateur)

MI1.04 Students can render the 3D structure of a biomolecule so as to explain the electronic origin of the different non‐covalent interactions. (Amateur)

MI1.05 As it relates to a particular rendered structure, students can rank the relative strengths of covalent and noncovalent interactions. (Amateur)

MI2.01 Students can identify regions of a biomolecule that are exposed to or shielded from solvent. (Novice)

MI2.02 Students can identify other molecules in the local environment (e.g. solvent, salt ions, metals, detergents, other small molecules) that impact a molecular interaction of interest. (Novice)

MI2.03 Students can predict the impact of other molecules in the local environment (e.g. solvent, salt ions, metals, detergents, other small molecules) on a molecular interaction of interest. (Amateur)

MI2.04 Students can predict the pKa of an ionizable group based on the influence of its local three-dimensional environment. (Amateur)

MI2.05 Students can propose a change to the local environment that would yield a desired change in a molecular interaction. (Expert)

MI2.06 Using molecular visualization tools, students can determine which intermolecular force is most critical to stabilizing a given interaction. (Expert)

A glycosylated peptide from the ice-binding protein (PDB ID: 3uyv) from an Arctic yeast with the amino acid and carbohydrate monomers shown in different colors.Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

Note that this theme was formerly called Monomer Recognition (MR).

MB1.01 Given a rendered structure of a biological polymer students can identify the ends of a biological polymer. (Novice, Amateur, Expert)

MB1.02 Given a rendered structure, students can divide the polymer into its individual building blocks. (Novice)

MB1.03 Given a rendered structure, students can identify the individual building blocks. (Novice)

MB2.01 Students can describe the physical properties of an individual building block in a rendered structure of a polymer. (Amateur)

MB2.02 Students can describe the significance of the location of individual building blocks within the 3D structure of a polymer (protein, carbohydrate or nucleic acid). (Novice, Amateur, Expert)

MB2.03 Students can identify an individual building block in a visualized structure that will interact with the surrounding environment (solvent and other molecules). (Amateur)

MB2.04 Using a visualized structure, students can identify stereochemical differences in carbohydrate structures. (Amateur)

MB2.05 Using a visualized structure, students can modify a building block to design it to have particular physical properties. (Expert)

[xxTODO]Recognition of symmetry elements within both single chain and oligomeric macromolecules.

SA1.01 Students can identify symmetric features in a rendered molecule (shown in fixed orientation). (Novice)

SA1.02 Students can rotate a given, rendered molecule and identify axes of symmetry. (Amateur)

SA1.03 Students can identify symmetric and asymmetric features in rendered molecules after coloring a given rendered molecule to reveal structural features (charge, hydrophobicity, etc.). (Amateur)

SA2.01 Students can explain functional significance of symmetry (or asymmetry) in a given rendered molecule. (Novice, Amateur, Expert)

SA2.02 Students can predict functional significance of symmetry (or asymmetry) in a given rendered molecule. (Amateur, Expert)

Active site residues of the serine protease, chymotrypsin (PDB ID: 1gg6), with the active site residues highlighted and a covalently bound amino acid substrate mimic.Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

SF1.01 Students can distinguish protein, cofactors and small molecule ligands or substrates. (Novice)

SF1.02 Students recognize that the size and shape of the ligand must match the size and shape of the binding site. (Novice, Amateur)

SF1.03 Students recognize that the polarity of a surface complements that of the ligand or substrate. (Novice, Amateur)

SF1.04 Students recognize that the hydrophobicity of a surface complements that of the ligand or substrate. (Novice)

SF1.05 Students recognize that the electrostatic potential of a surface can guide or direct the binding of a ligand or substrate. (Amateur)

SF1.06 Students can use docking software to predict how the surface properties of a macromolecule guides and allows the binding of a ligand or substrate. (Amateur)

SF2.01 Students can recognize structurally related molecules. (Novice)

SF2.02 Students can align structurally related molecules. (Novice, Amateur)

SF2.03 Students can identify functionally relevant features of a macromolecule. (Amateur)

SF2.04 Students can predict molecular function given a binding site. (Amateur, Expert)

SF2.05 Students can produce a model of a biomolecule based on a known structure of a related biomolecule. (Amateur, Expert)

SF3.01 Students can structurally alter a macromolecule. (Novice)

SF3.02 Students can propose structural alterations to test interactions in a macromolecule. (Amateur)

SF3.03 Students can predict the impact of a structural alteration on the function of a macromolecule. (Amateur, Expert)

[xxTODO]Recognition of the limitations of models to describe the structure of macromolecules.

SK1.01 Students can explain that the pdb file is a model based on data and that, as a model, it has limitations. (Novice, Amateur)

SK1.02 Students associate resolution with reliability of atom positions. (Amateur)

SK1.03 Students can identify building blocks (for example, amino acid sidechains) whose orientation in a macromolecule is uncertain. (Expert)

SK1.04 Students can evaluate the flexibility/disorder of various regions of a macromolecular structure. (Novice, Amateur, Expert)

SK1.05 Students can reconcile inconsistent numbering of individual building blocks among species and structure files. (Novice)

SK1.06 Students can utilize a Ramachandran plot to interpret the validity of a structure. (Amateur)

SK1.07 Students can describe the limitations of a macromolecule‐ligand docking simulation. (Expert)

SK2.01 Students can evaluate a crystal structure for crystal packing effects. (Novice, Amateur, Expert)

SK2.02 Students can resolve differences between the asymmetric unit and the functional biological assembly. (Expert)

SK2.03 Students can identify molecules present in a crystal structure that may not be associated with function. (Novice, Amateur, Expert)

SK3.01 Students can identify non‐native structural features. (Amateur)

SK3.02 Students can propose molecular modifications to facilitate structure determination. (Amateur, Expert)

SK3.03 Students can propose a purpose for the introduction of non‐native structural features to facilitate structure determination. (Amateur, Expert)

The zinc finger domains of a protein bound to RNA (PDB ID: 1un6).Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

TC1.01 Students can trace the backbone of a macromolecule in three dimensions. (Novice, Amateur)

TC1.02 Students can use appropriate terms to describe the linkages/bonds/interactions that join individual building blocks together in a macromolecule or macromolecular assembly. (Novice, Amateur)

TC1.03 Given a virtual model of individual building blocks, students can predict the types of linkages/bonds/interactions that are possible or favorable. (Amateur)

TC2.01 Using molecular visualization software, students can describe the three-dimensional structure of a macromolecule, including overall shape and common structural motifs. (Novice, Amateur, Expert)

TC2.02 Students can identify common domains/motifs within a macromolecule. (Amateur, Expert)

TC2.03 Students can identify connectivity features between domains or subunits in a macromolecular structure. (Amateur)

TC2.04 Students can identify interactions between domains or subunits in a macromolecular structure. (Amateur, Expert)

TC2.05 Students can describe how domains/motifs in a macromolecule work together to achieve a concerted function in the cell. (Amateur, Expert)

TC2.06 Students can parse a tertiary structure into a series of secondary structures and the ways in which they are connected from a three‐dimensional structure. (Novice, Amateur, Expert)

TC3.01 Students can recognize that the groups that comprise a functional site only require proper arrangement in three dimensional space rather than a particular order or position in the linear sequence. (Amateur)

TC3.02 Students can recognize similarities and differences in two similar ‐ but not identical ‐ three dimensional structures. (Amateur)

TC3.03 Students can describe dissimilar portions of homologous proteins as arising from genetic insertions/deletions/rearrangements. (Amateur)