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Presented by Hui Li Department of Chemistry University of Nebraska-Lincoln Jan 16, 2009

COMPUTATIONAL CORE. Presented by Hui Li Department of Chemistry University of Nebraska-Lincoln Jan 16, 2009. Necessity. Computer and information technologies have grown rapidly during the past few decades Created profound impact on biochemical research and analysis

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Presented by Hui Li Department of Chemistry University of Nebraska-Lincoln Jan 16, 2009

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  1. COMPUTATIONAL CORE Presented by Hui Li Department of Chemistry University of Nebraska-Lincoln Jan 16, 2009

  2. Necessity • Computer and information technologies have grown rapidly during the past few decades • Created profound impact on biochemical research and analysis • Computer-aided collection, transfer, and processing of large quantities of data • Exploration of information from a variety of bioanalytical databases • Molecular modeling based on quantum chemical and/or empirical force field methods

  3. Cyberinfrastructure • A common cyberinfrastructure will significantly enhance the accessibility, operation, management, and productivity of projects that are performed in the NCRB • This cyberinfrastructure will create a means by which data can be directly input and shared from various new and existing facilities, such as the Robotics & Automated Sample Preparation Core and the MS and NMR facilities at UNL, as well as the bioinformatics, functional analysis, and nanoimaging facilities at UNL and UNMC • Ready access to external connections and a means for outreach and dissemination of research results to the broader scientific community

  4. Computer-aided rapid bioanalysis • The Computational Core will complement and enhance the existing computing power at UNL and UNMC for work in rapid bioanalysis • Bioanalysis data obtained through modern analytical instruments (e.g., those used in mass spectrometry or NMR spectroscopy) will be important to many of the projects comprising the NCRB’s research portfolio • Significantly increase the ability of NCRB researchers to use the established bioinformatics facilities at UNL and UNMC

  5. Biomolecular simulation • Theoretical and computational methods have been increasingly employed in the study of biomolecules • Quantum mechanics and molecular mechanics calculations have reached a level of sophistication that can provide valuable insights into complex molecular systems, and often provide important guidance for experimental studies • The Computational Core will provide the processing capability for such calculations, as will be required by NCRB projects that involve either complex biomolecular systems or simulations of bioanalysis methods

  6. Core support for NCRB projects • This core will benefit all members of the NCRB • Modeling of single molecule tracking/imaging (Project 2 Bashford) • Creation of new data analysis methods (Projects 1 & 5 by Powers and Steinke) • Support planned new hires involving the characterization of complex biological systems through proteomics, metabolomics or glycomics • Existing faculty (Drs. Cerny, Du, Hage, Harbison, Lyubchenko, Redepenning)

  7. Core support for NCRB projects • Advanced quantum chemical calculations on biomolecules and molecular mechanics simulations of biomolecular systems will be immediately useful in Project 1 (Powers). • High-throughput drug screening, such as Projects 2 and 3 (Bashford and Cheung).

  8. Aims The Computational Core will contribute to NCRB’s overall success by completing the following specific aims: Aim 1: Provide a cyberinfrastructure for the proposed COBRE research and core facilities. Aim 2: Provide computing power and software support for analyzing data and simulating or optimizing new bioanalysis methods. Aim 3: Provide computing power and software support for molecular modeling to be used to examine data from bioanalysis methods. Aim 4: Provide training to faculty, graduate students, and post-doctoral fellows in use of the programs and facilities hosted within the Computational Core.

  9. Hardware Server • 100 computer processors • 400 gigabit memory • 30,000 gigabit disk storage space • A gigabit network for parallel computing • Uninterrupted power source User-end • Five user-end workstations for NCRB investigators • Graphics software necessary to visualize protein/macromolecular structures

  10. Software • Fortran and C compilers for researchers who wish to develop their own computer programs for the simulation or optimization of bioanalysis methods, as well as for creating new programs for data analysis; • Matlab with additional signal and image processing toolboxes for use in the modeling and optimization of bioanalysis methods; • Software for examining protein/macromolecular structures (e.g., AMBER, CHARMM, and Insight II) and protein-ligand docking experiments (e.g., AutoDock 4) for work involving proteomics, drug screening methods, or biointeraction studies

  11. Software • Software for use in calculations related to quantum chemistry (e.g., Gaussian and Gamess) and molecular mechanics software (e.g., AMBER and CHARMM) for electronic structure analysis and dynamic simulations of biomolecules, as could be used for work involving proteomics, drug screening methods, or biointeraction studies • Other software packages required by users.

  12. Management Director Hui Li, Department of Chemistry, UNL Research area: computational chemistry Duty: User training and tutorials System administrator A full-time post-doctoral fellow Formal system administration training Duty: daily management Location Department of Chemistry, UNL An existing computer room with heat exchange

  13. User friendly services • No charge to all users associated with the NCRB; A small fee to other users at UNL and UNMC • Users will be provided with convenient, continuous remote access • Consultation and training regarding quantum electronic structure calculations and molecular dynamics simulations • Tutorials on basic quantum chemistry, software use, input decks, job submission, and output analysis will be developed and/or posted by this core for use at the NCRB website

  14. Specific daily functions • Host the NCRB website, as updated and maintained by the Administrative Core. • Work with the Center Administrator to create a facility that will manage/share NCRB research reports and data. • Provide access to the other facilities at UNL and UNMC, such as the mass spectrometry and NMR facilities. • Provide computing power for performing simulations of new bioanalysis methods, as well as quantum calculations on biomolecules, molecular mechanics simulations for biomolecular systems, and drug-protein docking experiments. • Provide consultation and training pertaining to advanced computational chemistry methods

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