The homeobox genes that define the basic body plan of mice and fruit flies are illustrated in this graphic from The Human Evolution Coloring Book by Adrienne Zihlman. The accompanying article describes how these genes act as molecular architects in all animal species.

Study and discussion of computational approaches and algorithms for contemporary problems in functional genomics. Topics include DNA chip design, experimental data normalization, expression data representation standards, proteomics, gene clustering, self-organizing maps, Boolean networks, statistical graph models, Bayesian network models, continuous dynamic models, statistical metrics for model validation, model elaboration, experiment planning, and the computational complexity of functional genomics problems.

As a class, students work through an example showing how DNA provides the "recipe" for making our body proteins. They see how the pattern of nucleotide bases (adenine, thymine, guanine, cytosine) forms the double helix ladder shape of DNA, and serves as the code for the steps required to make genes. They also learn some ways that engineers and scientists are applying their understanding of DNA in our world.

This narrated animation schematically shows the process of protein synthesis. Adapted from Interactive NOVA: "Secret of Life."

Student teams learn about engineering design of green fluorescent proteins (GFPs) and the use of GFPs in medical research, including stem cell research. The use of GFPs is simulated by adding fluorescent dye to water and allowing a flower or plant to transport the dye throughout its structure. Students apply their knowledge of GFPs to engineering applications in the medical, environmental and space exploration fields. Due to the fluorescing nature of the dye, plant life of any color, light or dark, can be used unlike dyes that can only be seen in visible light.

This module provides a brief introduction to the classes of protein interactions that mediate biological processes, with examples.

From The Human Evolution Coloring Book by Adrienne Zihlman, four different proteins from humans and horses are compared in this graphic and article, and the reasons each protein evolves at its own characteristic rate are discussed. Each protein is useful for measuring evolutionary change over a different time scale.

This module introduces students to a family of algorithms for assessing molecular shape, volume, surface area, and negative space (i.e., pockets and cavities).

Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. This course, intended for both graduate and upper level undergraduate students, will focus on understanding of the basic molecular structural principles of biological materials. It will address the molecular structures of various materials of biological origin, such as several types of collagen, silk, spider silk, wool, hair, bones, shells, protein adhesives, GFP, and self-assembling peptides. It will also address molecular design of new biological materials applying the molecular structural principles. The long-term goal of this course is to teach molecular design of new biological materials for a broad range of applications. A brief history of biological materials and its future perspective as well as its impact to the society will also be discussed. Several experts will be invited to give guest lectures.

This module introduces the concept of free energy and potential fields in the context of protein conformation spaces and motion planning. It then provides examples of applications of motion planning techniques to problems from structural computational biology.

Nutrients (raw materials) are chemical substances found in foods. Essential nutrients are those that the body cannot make or is unable to make in the amount it needs. The 50 or so essential nutrients people need can be grouped into 6 basic categories and include protein, carbohydrates, fat, vitamins, minerals, and water.

This course focuses on the latest scientific developments and discoveries in the field of nanomechanics, the study of forces and motion on extremely tiny (10-9 m) areas of synthetic and biological materials and structures. At this level, mechanical properties are intimately related to chemistry, physics, and quantum mechanics. Most lectures will consist of a theoretical component that will then be compared to recent experimental data (case studies) in the literature. The course begins with a series of introductory lectures that describes the normal and lateral forces acting at the atomic scale. The following discussions include experimental techniques in high resolution force spectroscopy, atomistic aspects of adhesion, nanoindentation, molecular details of fracture, chemical force microscopy, elasticity of single macromolecular chains, intermolecular interactions in polymers, dynamic force spectroscopy, biomolecular bond strength measurements, and molecular motors.

In this video segment from An Introduction to the Living Cell, explore the inner workings of a cell, including some of its most important organelles.

In this laboratory exercise, students utilize differential precipitation and polyacrylamide gel electrophoresis in combination with centrifugation and detergent extraction to fractionate the complex mixtures of proteins found in mammalian red blood cells and mammalian blood plasma and to characterize some of the component proteins. Gels are stained with Coomassie blue and migration distances for the unknown proteins are compared with those of known protein standards. Students then determine the sizes of the unknown proteins, compare their relative abundance, speculate about the identities of the components of the various fractions, and evaluate the efficiency of the fractionation techniques.

This module introduces students to inverse kinematics, which is the problem of finding values of the degrees of freedom of a manipulator chain so that the chain satisfies given spatial constraints. An application of inverse kinematics to solve the loop closure problem in structural biology is also presented.

This module provides a high-level introduction to the field of protein-ligand docking, then provides examples of a few rigid-receptor docking methods, and introduces some techniques which are being developed to allow receptor flexibility.

This module discusses how to represent proteins in terms of the Cartesian coordinates of their atoms and in terms of the angle values of their rotatable bonds. It then discusses Forward Kinematics, which allows the computation of Cartesian coordinates whe

This module explains how to model a protein as a robotic manipulator and introduces the robotic path planning problem and algorithms for solving it, including the probabilistic roadmap method. Variations of the Probabilistic Roadmap Method have been employed for problems related to protein motion.

This module contains motivational and biochemical background material for a computer scientist beginning to learn about computational structural biology.