The Center for the Study of Systems Biology, CSSB is poised to be a central player in an emerging revolution in biology

The goals of the CSSB are:

  • In the very long term, to be able to simulate and understand how life works
  • To develop and identify novel approaches to the diagnostics and treatment of diseases especially cancer
  • To develop a novel parallel approach to the development of drugs
  • To develop novel approaches to protein pathway engineering based on microfluidics using state of the art protein chips and biosensors

Collections in this community

Recent Submissions

  • Drug Discovery Accelerated by Computational Methods 

    Jorgensen, William L. (Georgia Institute of Technology, 2013-04-30)
    Drug discovery is being pursued through computer-aided design, synthesis, biological assaying, and crystallography. Lead identification features de novo design with the ligand growing program BOMB or docking of commercial ...
  • Mapping Protein Folding on Organismal Fitness One Mutation at a Time 

    Shakhnovich, Eugene (Georgia Institute of Technology, 2013-03-12)
    In this presentation I will describe our efforts at understanding how molecular properties of proteins determine fitness landscape of populations of carrier organisms. Recent multi-scale evolutionary models, which assume ...
  • Histone Variants, Nucleosome Dynamics and Epigenetics 

    Henikoff, Steven (Georgia Institute of Technology, 2013-02-12)
    The Henikoff Lab's recent studies have aimed to understand the elusive relationship between chromatin and epigenetic inheritance. In large part, their focus has been on the universal set of histone variants that replace ...
  • Structural Basis for Iron Piracy by Pathogenic Neisseria 

    Buchanan, Susan (Georgia Institute of Technology, 2012-10-16)
    Neisseria are obligate human pathogens causing bacterial meningitis, septicemia, and gonorrhea. Neisseria require iron for survival and can extract it directly from human transferrin for transport across the outer membrane. ...
  • Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations 

    Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2012-08)
    Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. ...
  • Development and Evolution of Vertebrate Development and Evolution of Vertebrate 

    Tabin, Clifford (Georgia Institute of Technology, 2012-04-24)
    Dr. Tabin's laboratory studies the genetic basis by which form and structure are regulated during vertebrate development. They combine classical methods of experimental embryology with modern molecular and genetic techniques ...
  • GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction 

    Zhou, Hongyi; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2011-10)
    An accurate scoring function is a key component for successful protein structure prediction. To address this important unsolved problem, we develop a generalized orientation and distance-dependent all-atom statistical ...
  • The ESCRT pathway in HIV Budding and Cell Division 

    Sundquist, Wesley (Georgia Institute of Technology, 2012-01-31)
    The Endosomal Sorting Complexes Required for Transport (ESCRT) pathway mediates intraluminal endosomal vesicle formation, budding of HIV-1 and other enveloped viruses, and the final abscission step of cytokinesis in mammals ...
  • New approaches to studying the growth and size regulation of mammalian cells 

    Kirschner, Marc (Georgia Institute of Technology, 2012-01-24)
    The study of cell growth has been limited primarily by the lack of accurate enough means of measuring the growth of cells as they traverse the cell cycle. There are several theoretical models of growth that have been ...
  • New Biology from Natural Metamorphosis of a Conventional Class of Enzymes 

    Schimmel, Paul (Georgia Institute of Technology, 2011-11-15)
    A group of enzymes known as aminoacyl tRNA synthetases interpret genetic information through catalysis of aminoacylation reactions that establish the genetic code. Errors of interpretation are corrected by a universal ...
  • Protein Folding Inside Cells and Other Crowded Environments 

    Gruebele, Martin (Georgia Institute of Technology, 2011-11-08)
    Computer simulations are reaching the point where folding of small proteins in vitro can be successfully achieved ‘ab initio’ by molecular dynamics. Experiments can help further calibrate simulations, and I will discuss ...
  • An object oriented environment for artificial evolution of protein sequences: The example of rational design of transmembrane sequences 

    Milik, Mariusz; Skolnick, Jeffrey (Georgia Institute of TechnologyMassachusetts Institute of Technology Press, 1995)
    A system is presented for generating peptide sequences with desirable properties, using combination of neural network and artificial evolution. The process is illustrated by an example of a practical problem of ...
  • Optimization of protein structure on lattices using a self-consistent field approach 

    Reva, Boris A.; Rykunov, D. S.; Finkelstein, Alexei V.; Skolnick, Jeffrey (Georgia Institute of TechnologyMary Ann Liebert, Inc., 1998)
    Lattice modeling of proteins is commonly used to study the protein folding problem. The reduced number of possible conformations of lattice models enormously facilitates exploration of the conformational space. In this ...
  • The dependence of all-atom statistical potentials on structural training database 

    Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi (Georgia Institute of TechnologyBiophysical Society, 2004-03)
    An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, ...
  • TASSER_WT: A protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets 

    Lee, Seung Yup; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2010-11)
    To improve the prediction accuracy in the regime where template alignment quality is poor, an updated version of TASSER_2.0, namely TASSER_WT, was developed. TASSER_WT incorporates more accurate contact restraints from a ...
  • Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model 

    Kolinski, Andrzej; Klein, Piotr; Romiszowski, Piotr; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-11)
    Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to experiment. The models ...
  • Application of sparse NMR restraints to large-scale protein structure prediction 

    Li, Wei; Zhang Yang; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2004-08)
    The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated ...
  • TOUCHSTONE II: a new approach to ab initio protein structure prediction 

    Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey (Georgia Institute of TechnologyBiophysical Society, 2003-08)
    We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting Ca atoms, with attached Cb atoms and side-chain centers of mass. The ...
  • Onset of anthrax toxin pore formation 

    Gao, Mu; Schulten, Klaus (Georgia Institute of TechnologyBiophysical Society, 2006-05)
    Protective antigen (PA) is the anthrax toxin protein recognized by capillary morphogenesis gene 2 (CMG2), a transmembrane cellular receptor. Upon activation, seven ligand-receptor units self-assemble into a heptameric ...
  • Simulated refolding of stretched titin immunoglobulin domains 

    Gao, Mu; Lu, Hui; Schulten, Klaus (Georgia Institute of TechnologyBiophysical Society, 2001-10)
    Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin I27, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to ...

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