Training Spotlights

Summer School in Urbana, Illinois. Modeling the molecular processes of biological cells is a craft and an art. Techniques like theoretical and computational skills can be learnt by training, but meaningful applications are achieved only with experience and sensitivity. A summer school held June 2-13, 2003 in Theoretical and Computational Biophysics attempted to teach both the craft and art of modeling through learning by doing: nearly a hundred participants from all over the world came for two weeks to the Beckman Institute in Illinois to stretch proteins, pull water through molecular channels, mine genomic data, build their own computer cluster, and study their favorite biomolecules.

Hands-on Workshop in Perth, Australia. In June 2004, at the University of Western Australia in Perth, the Theoretical and Computational Biophysics Group offered a workshop in computational biophysics, attempting to teach both the craft and art of modeling through learning by doing. Twenty-seven participants attended the workshop, to stretch proteins, pull water through molecular channels, mine genomic data, and to study their favorite biomolecules.

Hands-on Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop, attempting to teach both the craft and art of modeling through learning by doing. During the week of November 8-12, 2004, 21 participants attended the workshop at the University of Illinois, in the Beckman Institute for Advanced Science and Technology. Participants learned how to stretch proteins, pull water through molecular channels, mine genomic data, and study biomolecules.

Hands-on Workshop in Boston, Massachusetts. Theoretical and computational skills can be learned via training, but meaningful applications are achieved only with experience and sensitivity; in that sense, modeling the molecular processes of biological cells is a craft and an art. In Boston, Massachusetts, during early December 2005, the Theoretical and Computational Biophysics Group offered a workshop, attempting to teach both the craft and art of modeling through learning by doing. Participants learned through lectures and hands-on tutorial sessions how to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules.

Hands-on Workshop in Chicago, Illinois. Meaningful applications of learned theoretical and computation skills are achieved only with experience and sensitivity. The Theoretical and Computational Biophysics Group offered a workshop in Chicago, Illinois, June 9-13, attempting to teach both the art and craft of molecular modeling through learning by doing. Morning lectures and afternoon tutorials helped participants learn how to stretch proteins, pull water through molecular channels, mine genomic data, and study biomolecules, and generally arming participants with tools to advance their own research.

Hands-on Workshop in Tahoe City, California. The beautiful Lake Tahoe area was the site of a May 2005 workshop held by the Theoretical and Computational Biophysics Group, that attempted to teach both the craft and art of molecular modeling. A learning-by-doing approach utilized morning lectures with hands-on tutorial sessions in the afternoon, providing participants opportunities to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules on laptops humming with computational biology software, e.g. VMD and NAMD.

Hands-on Workshop in San Francisco, California. At the end of June 2005, a workshop attempting to teach the craft and art of molecular modeling was conducted by the Theoretical and Computational Biophysics Group in San Francisco California. An agenda of morning lectures followed by related hands-on tutorial sessions in the afternoon gave the 20 participants the opportunity to develop the experience and sensitivity needed for meaningful applications of their newly-gained theoretical and computational skills. Working on laptops humming with computational biology software, e.g. VMD and NAMD, participants were able to stretch proteins, pull water through molecular channels, mine genomic data, build their own computer cluster, and study their favorite biomolecules.

Hands-on Workshop at the Pittsburgh Supercomputing Center. From November 29 - December 1, 2005, a workshop attempting to teach the craft and art of molecular modeling was conducted by the Theoretical and Computational Biophysics Group at the Pittsburgh Supercomputing Center in Pittsburgh, Pennsylvania. An agenda of morning lectures followed by related hands-on tutorial sessions in the afternoon gave the 24 participants the opportunity to develop the experience and sensitivity needed for meaningful applications of their newly-gained theoretical and computational skills. Working at computer stations humming with computational biology software, e.g. VMD and NAMD, participants were able to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules.

Hands-on Workshop in Frankfurt, Germany. From March 20-23, 2006, a workshop attempting to teach the craft and art of molecular modeling was conducted by the Theoretical and Computational Biophysics Group at the Max Plank Institute in Frankfurt, Germany. An agenda of morning lectures followed by related hands-on tutorial sessions in the afternoon gave the 24 participants the opportunity to develop the experience and sensitivity needed for meaningful applications of their newly-gained theoretical and computational skills. Participants worked on their own laptops humming with computational biology software, e.g. VMD and NAMD, and were able to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules.

Hands-on Workshop in Pittsburgh. From November 6-9, 2006, a workshop attempting to teach the craft and art of molecular modeling was conducted by the Theoretical and Computational Biophysics Group at the Department of Structural Biology at the University of Pittsburgh in Pittsburgh, Pennsylvania. An agenda of morning lectures followed by related hands-on tutorial sessions in the afternoon gave participants the opportunity to develop the experience and sensitivity needed for meaningful applications of their newly-gained theoretical and computational skills. Working at computer stations humming with computational biology software, e.g. VMD and NAMD, participants were able to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules.

Hands-on workshop in Talca, Chile. Modeling the molecular processes of biological cells is a craft and an art. Techniques like theoretical and computational skills can be learnt by training, but meaningful applications are achieved only with experience and sensitivity. The Theoretical and Computational Biophysics Group offered a workshop, attempting to teach both the craft and art of modeling through learning by doing. Forty participants attended the workshop held at the University of Talca in Talca, Chile, and sponsored by the Centro de Bioinformática y Simulación Molecular (CBSM), the Centro de Genomica y Bioniformatica, and Fondecyt. Participants learned how to simulate biological and synthetic membrane channels, stretch proteins, make publication quality images and movies, and study their favorite biomolecules. After lectures and discussions in the morning, afternoons were devoted to tutorials providing hands-on experience with lecture concepts, in prepared computers labs installed with needed computational biology software, e.g., VMD and NAMD.

Hands-on workshop in Bethesda. Modeling the molecular processes of biological cells is a craft and an art. Techniques like theoretical and computational skills can be learnt by training, but meaningful applications are achieved only with experience and sensitivity. Helix Systems, of the Center for Information Technology at the National Institutes of Health (NIH) and the NIH Resource for Macromolecular Modeling and Bioinformatics offered a workshop, attempting to teach both the craft and art of modeling through learning by doing. Thirty participants attended the workshop held in Building 12A, Room B51, at the main NIH campus in Bethesda, Maryland. Participants learned how to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules. After lectures and discussions in the morning, afternoons were devoted to hands-on computer laboratories where participants delved into over 200 pages of tutorials, on their own laptops or laptops provided for the workshop, all humming with computational biology software, e.g., VMD and NAMD

Hands-on workshop in Bangalore. In the workshop at Bangalore, India, TCBG member Aruna Rajan traveled to the Centre for Computational Materials Science (CCMS) at the Jawaharlal Nehru Centre for Advanced Scientific Research to lecture and provide tutorial instruction alongside instructors from other institutions, using TCBG and other training materials. Here is CCMS's description of the event: "The scope of the school is to introduce methods and tools in setting up molecular simulations in context of biomolecules. Using molecular dynamics methodology as the central concept, the school aims at providing a systematic way to setup the systems, simulating them, analysis techniques to extract and visually represent some of the interesting properties of biological systems. Some of the biological systems that may be explored will include DNA, ion channels, lipid membranes etc. Familiarity with basic thermodynamics, UNIX and basic programming will be assumed. However the school will have introductory sessions on aspects of molecular simulations such as molecular dynamics methodology, force fields, ensemble representation etc. The morning sessions will have lectures introducing concepts and methods and the afternoon sessions will have computational exercises. The school will be based on freely available software NAMD (www.ks.uiuc.edu) and VMD. The school will also include lectures on applications of computer simulations to biological problems of current interest."

TCB Computational Biology Workshops. To guide cell biology research and explain observation through molecular structures and sequence data, life scientists resort increasingly to computational tools. Sequence and structure viewers (VMD) combined with molecular dynamics modeling software (NAMD) are primary methodologies that revolutionized modern biomedicine. The revolution happened so quickly, though, that traditional university training has not kept up with the pace of developments in computational biology. A series of computational biophysics workshops in Perth (Australia), Urbana, Boston, Lake Tahoe, Chicago, and San Francisco attempted to fill the gap through hands-on training. Theory sessions in the morning introduced the concepts and methods used in molecular modeling today; computer laboratories in the afternoon gave participants, students, postdocs, and faculty, opportunities to work through tutorials at their own pace on provided laptops, as well as work on their own research problems. The workshops funded by NIH, NSF, NCSA, UIUC, and UWA met the needs of novices and experts alike for instruction in a new generation of research methods. All workshop materials are available on the web.

Portable Workshop Computing Lab. Supporting the ’hands-on’ computational and visualization needs of the workshops required a solution that not only provided sufficient computational power, but that also provided high-quality graphics, and that was reasonably portable. The Resource purchased with local funds 22 Macintosh PowerBook G4’s with 15-inch monitor displays, 80 gigabyte hard drives, and memory upgraded by Resource members to 768 megabytes. Tutorial-required software including VMD, NAMD, Mathematica, Matlab and Spartan was installed on each laptop to provide users with easy access to these tools when working on the tutorials. Files required by the tutorials were also installed on the hard drive, as were instruction and copies of the tutorial texts. At each workshop, teaching assistants set up the laptops for the 20 participants, with the remaining two laptops used by the instructors for demonstrations and leading participants through lectures and tutorials. In this fashion, all participants were provided with needed learning resources, without the workshop having to rely on local availability of computer labs.

Cluster Building Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop on cluster building, on September 22-23, 2005 at the Beckman Institute in Urbana, Illinois. The day and a half workshop helped users and system administrators specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually built their own PC clusters and got to test out their own applications.

[September 2005 Urbana Cluster Building Workshop]

Cluster Building Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop on cluster building, on November 10-11, 2005 at the Beckman Institute in Urbana, Illinois. The day and a half workshop helped users and system administrators specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually built their own PC clusters and got to test out their own applications.

[November 2005 Urbana Cluster Building Workshop]

Cluster Building Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop on cluster building, on March 16-17, 2006 at the Beckman Institute in Urbana, Illinois. The day and a half workshop helped users and system administrators specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually built their own PC clusters and got to test out their own applications.

[March 2006 Urbana Cluster Building Workshop]

Cluster Building Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop on cluster building, on April 20-21, 2006 at the Beckman Institute in Urbana, Illinois. The day and a half workshop helped users and system administrators specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually built their own PC clusters and got to test out their own applications.

[April 2006 Urbana Cluster Building Workshop]

Cluster Building Workshop in Urbana, Illinois. The Theoretical and Computational Biophysics Group offered a workshop on cluster building, on November 30 - December 1, 2006 at the Beckman Institute in Urbana, Illinois. The day and a half workshop helped users and system administrators specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually built their own PC clusters and got to test out their own applications.

[Nov-Dec 2006 Urbana Cluster Building Workshop]

February 2007 Online Workshop. Modeling and simulation of molecular systems has become an inseparable component of modern research. In particular, molecular dynamics simulation is increasingly used to investigate the molecular mechanism of function and structure-function relationship of a wide range of biological macromolecules. The Theoretical and Computational Biophysics Group offered a online workshop, providing a brief introduction to such methodologies, and using membrane channels as an example of how theoretical biophysical methods and computer simulation technology can be applied to biological problems. Examples used in the class included aquaporin water channels as an example for biologically relevant materials, as well as carbon nanotubes as artificial materials. Modeling, simulation setup, and analysis of the results was demonstrated along with the lessons learnt from simulation studies of these systems. A streaming lecture was accompanied by a hands-on tutorial in which participants set up and ran small simulations on their own, using the TCBG's computational biology software, VMD and NAMD.

VMD Tutorial. The VMD Tutorial introduces new users to VMD and its capabilities. It can also be used as a refresher course for the occasional VMD user wishing to employ this program more productively. The tutorial is subdivided into three separate units of increasing complexity. The first unit covers the basics of molecular graphics representations and will introduce everything you need to know to generate nice graphics. The other two units are targeted toward the scientifically-oriented user and focus on scripting in VMD. While scripting may be skipped by the non-technical users, we encourage everyone to give it a try as it provides some very powerful (and easy to use) tools that cannot be offered by a simple graphical user interface.

NAMD Tutorial.The NAMD tutorial provides a first introduction to NAMD and its basic capabilities. It can also be used as a refresher course for the non-expert NAMD user. It is subdivided in three sections. The first section covers the basic initial steps of a molecular dynamics simulation, the minimization and equilibration of your system, and describes NAMD's user options and output. The second section introduces typical simulation techniques and the analysis of properties for molecular systems. The third section introduces Steered Molecular Dynamics and the analyis of unfolding pathways of proteins. Finally, descriptions of all files needed for the simulations are provided in the appendices.

Evolution of Protein Structure: Asparty-tRNA Synthetase Tutorial. The Evolution of Protein Structure tutorial showcases the new software tools in Multiple Alignment in VMD. Multiple Alignment is an invaluable tool for relating protein structure to its function or misfunction. This tutorial focuses on the examination of the correlation of sequence and structure changes and representing these changes in terms of structural phylogenetic trees.

Aquaporins with the VMD Multiseq Tool Tutorial. Introduces participants to the VMD MultiSeq Tool, which links protein structures to protein sequences and allows users to compare proteins in terms of structure and sequence. The aquaporin family of membrane proteins, found in a wide range of species including humans, are used for a case study of the applications of the MultiSeq tool. Specifically, the tool is used to conduct a comparative study of the structure and sequence of four aquaporins from different species: human AQP1, bovine AQP1, AqpZ from E.coli, and GlpF (E.coli glycerol facilitator).

Bioinformatics and Sequence Alignment Tutorial. Bioinformatics uses the statistical analysis of protein sequences and structures to help annotate the genome, to understand their function, and to predict structures when only sequence information is available. Bioinformatics methods are used in fundamental research on theories of evolution and in more practical considerations of protein design. The tutorial begins with classical pairwise sequence alignment methods using the Needleman-Wunsch algorithm, and ends with the multiple sequence alignment available through CLUSTAL W.

Parameterizing a Novel Residue Tutorial. Inevitably there comes a time in any molecular modelling scientist's career when the need to simulate an entirely new molecule or ligand arises. The technique of determining new force field parameters to describe these novel system components therefore becomes an invaluable skill. Determining the correct system parameters to use in conjunction with the chosen force field is only one important aspect of the process. The ability to use several programs simultaneously to examine and refine the system in question is also a critical element of these kinds of problems. This tutorial will walk you through a comprehensive example of how one investigates, sets up, and simulates a small nonstandard ligand bound to a protein system; specifically, we will investigate the glutaminase subunit of the hisH-hisF system and will determine parameters for its covalently bound substrate.

Topology File Tutorial. Often, one encounters the need in molecular dynamics to simulate molecules for which topology and parameter information does not exist. In many cases, parameter development is necessary, but in others it may not be. This tutorial introduces how to create this information based on existing topology information for other molecules, without the need for new parameter development. The tutorial is subdivided in three sections. The first one introduces the method of topology file creation and situations when it is appropriate and inappropriate. The second section utilizes the method to create a topology file for a tripeptide bound to an enzyme and performs a simulation of the system. The last section provides the solution to a topology file creation problem posed in the tutorial. A working knowledge of VMD is assumed of those utilizing the tutorial, and later sections assume NAMD has been correctly installed on the user's computer.

Simulation of Water Permeation through Nanotubes Tutorial. In this tutorial, participants will be investigating the permeation of water through nanotubes, as a model for transmembrane permeation of substrates through channels. Participants will observe water movement through an array of nanotubes under two types of simulation conditions, namely, free water diffusion in equilibrium and directional water flow under a hydrostatic pressure difference. Next, participants are taught how to 'decorate' nanotubes using AutoIMD, by modifying and experimenting with charge and charge configurations, and by modifying and experimenting with VdW parameters.

Stretching Deca-Alanine Tutorial. In this tutorial, participants are introduced to interactive molecular dynamics (IMD) and steered molecular dynamics (SMD) simulations, and to the calculation of potential of mean force (PMF) from trajectories obtained with SMD simulations. One system is used throughout the tutorial: deca-alanine, a peptide composed of ten alanine residues. Deca-alanine is simulated in a vacuum, where it forms an alpha-helix, and using IMD and SMD, participants stretch the molecule by applying an external force, and using SMD trajectories and employing Jarzynski's equality, the PMF involved in the helix-coil transition is calculated.

VMD Images and Movies Tutorial. This tutorial is designed to give users of VMD an introduction to advanced techniques for making custom images and movies. The first section looks at how to use features such as resolution, color, and material, depth perception, and volumetric data to produce effects and enhancemants for still images. The second part demonstrates how to work with trajectories, by using techniques such as smoothing trajectories, showing multiple frames at once, and making atom selections "follow" a trajectory. It also shows how to create a movie file from a trajectory using VMD's Movie Maker plugin.

Bionanotechnology Tutorial. This tutorial is designed to guide users of VMD and NAMD in all the steps required to set up a molecular dynamics (MD) simulation of a bionanotechnology device. While structure building for biomolecules is likely familiar to most VMD and NAMD users, constructing models of solid-state inorganic systems requires a slightly different approach. The tutorial starts in the first unit by teaching readers how to build models of synthetic devices, starting with only a crystal unit cell. The second unit guide readers through combining a biomolecule (DNA) with a crystalline membrane and simulating the resulting system.

User-Defined Forces in NAMD. The Forces tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts. These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions.

Membrane Proteins Tutorial. This tutorial is designed to guide users of VMD and NAMD through all the steps required to set up a membrane protein system for molecular dynamics simulations. The tutorial is subdivided into three separate units. The first unit covers steps required to set up a structural model of a membrane protein starting from a raw PDB file. The second unit describes the steps needed to place the protein in a native-like membrane environment. Finally, the third unit describes the steps required to minimize and equilibrate the resulting system with NAMD.

Aquaporins Case Study. In the Aquaporin case study, readers explore the secondary structure of aquaporins in their native membrane/water environment. Different aquaporins are structurally aligned using VMD and the \plugin{MultiSeq} plugin, with all the necessary files provided. The reader also learns what can be revealed from simulations of water conduction through the aquaporin, including how protons are prevented from crossing the membrane.

BPTI Case Study. Bovine pancreatic trypsin inhibitor (BPTI) is examined through extensive structural analysis, notably residue contact maps and alignment of structurally similar proteins. Readers also explore the stability of the protein in its oxidized and reduced forms at different temperatures, thus realizing a possible role of three key disulfide bonds present in the protein. Finally, the reader learns about the charge relay system of trypsin protease and how BPTI inhibits it via binding.

DNA Case Study. The DNA case study first helps the reader explore the different types of DNA and their unique structural properties using VMD's visualization and measurement capabilities. The analysis is then extended to higher order structures such as DNA wrapped around a histone or packed into chromatin. Various polymer models of DNA are explained and the reader explores the models hands-on, with provided data used for parameter fitting with VMD. Also, the mechanisms of sequence-specific protein binding to DNA are described with the reader examining the "zinc-binding" motif in more detail.

Lipid Bilayers Case Study. In the Lipid Bilayers case study, lipids are introduced and many structures are provided, allowing the reader to visualize their similarities and differences in VMD. The reader also learns about the properties of bulk lipid membranes. Membrane phases are described, along with lateral diffusion within a bilayer and specific lipid-lipid interactions. Additionally, the role of energetics in membrane protein placement in a bilayer is examined. In each case, files and instruction are provided for the reader to calculate various properties and investigate membrane features themselves.

Myoglobin Case Study. Myoglobin is a structurally rich protein, with many examples from various species known. To find the functionally most relevant parts of the protein, the Myoglobin case study examines myoglobin structure conservation using the MultiSeq plugin of VMD. Readers are also asked to form a hypothesis for oxygen entry into myoglobin; they then test this hypothesis by exploring the protein in detail. Finally, the more advanced reader can calculate a Mössbauer spectrum using provided simulation data.

Titin Case Study. The mechanical role of titin is very important in preventing muscle fiber over-extension. With this in mind, the reader explores the process of unfolding titin. By comparing experimental AFM unfolding data with simulation unfolding data of titin and the related protein telethonin, the reader discovers how the specific $\beta$-sheet structure gives the proteins the ability to withstand mechanical stress. Furthermore, the nature of hydrogen bonds in these structures is examined in detail; the reader observes how water mediates the breaking of such bonds and also how they reform between different pairs of residues using trajectories taken from simulation.

Ubiquitin Case Study. In the Ubiquitin case study, the protein signaling tag ubiquitin is used as a prototype for assorted computational biology investigations. The reader learns about common protein folds using structure and sequence alignment in the VMD \plugin{MultiSeq} plugin, and also sees the electrostatic environment of a proteasome with VMD's PME potential map. The reader also makes Ramachandran plots to learn about peptide torsion angles, builds a crystallographic unit cell in VMD, calculates protein stability over time, and analyzes SMD-induced unfolding using both visual observations of an example simulation and fitting a mathematical polymer model to the data.

Water Case Study. In the Water case study, the reader investigates the detailed molecular properties of water. Simulated structures of bulk water are provided so that the reader may examine water phases and hydrogen bonding patterns, and also study the binding of antifreeze proteins to ice. The pair distribution function is explored by the reader using VMD and provided analysis scripts. Also, given water's important role in biomolecular simulations, various computational water models are discussed. The reader then measures different model parameters and examines how they affect simulations of water at different temperatures.

Ion Channels Case Study. The physiological function of ion channels had been observed long before they were known to exist. Many cells such as nerve and muscle cells, were known to have excitable cell membranes that would respond to variations in their electrical membrane potential through an all-or-nothing response. It was soon discovered that the regulators of ion passage across biological membranes were specialized proteins called ion channels. Ion channels are transmembrane proteins that selectively allow a given species of ions to pass through them...

Light Harvesting Complex 2 Case Study. Sunlight is ultimately the energy source for nearly all life on Earth. Many organisms, such as plants, algae, and some bacteria, have developed a means to harvest sunlight and turn it into chemical energy, a process known as photosynthesis. Photosynthesis occurs with an amazingly high efficiency, not surprising given the more than 3.5 billion years of evolution...

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