Group Leaders      Dr. Werner Braun, Prof.      Dr. Catherine Schein, Associate Prof.          Research Homepage Group Members      Numan Oezguen, Dr. rer. nat.*      Ovidiu Ivanciuc, Ph.D.      David Power, Ph.D.      Surendra Negi, Ph.D.      Deliang Chen, Ph.D.      Tzintzuni I. Garcia      Aurora Ruiz, Office Assistant            *Dr. rerum naturalium	Welcome to the Computational Biology Homepage!
Former Group Members Click Here	The Computational Biology Group Outside Clay Hall (from left to right); David Power, Tzuni Garcia, Yuan Xu, Catherine Schein, Numan Oezguen, CJ Orlea, Ovidiu Ivanciuc, Werner Braun,  Bin Zhou, Deliang Chen, Milind Misra and Surendra Negi.

 
     Educational Materials

• Computer Modeling of Macromolecular Structure and Function 2008

• The Computational Biology Facility is located on the second floor of Clay Hall (listed as Building 31 on the  official campus map).  Classes meet in the Conference Room (2.130).

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     Braun Group Publications

• Recent publications
• Complete List

     Recent Group Presentations

• Click Here
  

 
     Internal Group Research Resource (Password Protected)

     Equipment Documentation and Supplies (Password Protected)

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     Research Projects

• PCPMer is a software tool for automatic motif detections of a protein family and identifications of related family members in protein sequence databases. (Catherine H. Schein and Werner Braun).
  
• Structural Biology of Allergens: Investigations regarding sequence and structural determinants of allergenicity, allergens motifs, and database mining for the identification of potential allergens (Ovidiu Ivanciuc, Catherine H. Schein, Terumi Midoro-Horiuti, Randall M. Goldblum, Edward G. Brooks, Werner Braun) 
• DNA Repair: Molecular recognition of DNA damage sites by apurinic/apyrimidinic endonucleases (Catherine H. Schein, Numan Oezguen, Tadehide Izumi, David Power, Werner Braun)
• FANTOM: software for efficient molecular modeling of proteins in torsional angle space
  (Kizhake Soman and Werner Braun).
• NOAH/DIAMOD, a suit of programs have been developed for automated 2D or 3D protein NOESY spectrum assignment and 3D structure determination (Numan Oezguen, Catherine H. Schein and Werner Braun).
• MASIA/DIAMOD development: An expert system which combines Self-Correcting Distance Geometry calculations with a pattern recognition algorithm to model 3D structures of protein
  (Catherine H. Schein and Werner Braun).
• Motif and Molego Analysis Project: Developing a GUI-interfaced program to search for consistent patterns in multiple aligned sequences. (Surendra Negi, Catherine H. Schein and Werner Braun).
• Bacillus anthracis Project: Sequence decomposition of the 3 toxins of B. anthracis is used to: identify conserved residues and likely interacting protein sites, yield conserved functional areas that differ from mammalian proteins with similar activities and to guide design of novel inhibitors to 1) complex formation and 2) catalytic activities
  (Deliang Chen, Catherine H. Schein, Johnny W. Peterson and Werner Braun).
  

     Software from Our Group

• MPACK is a homology modeling package that integrates several packages from our group: PCPmer to identify conserved regions, EXDIS to extract angle and distance constraints, DIAMOD to generate protein models from geometric constraints, and FANTOM to optimize the protein geometry with the ECEPP force field.
  
• SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics and computational tools to perform structural studies related to allergens and characterization of their epitopes.
• FANTOM (Energy refinement and Monte Carlo simulations of proteins).
• GETAREA (Web interface to solvent accessible surface area calculations).
• On-line Publication: Fraczkiewicz, R. and Braun, W. "A New Efficient Algorithm for Calculating Solvent Accessible Surface Areas of Macromolecules".
• MASIA (Pattern search and analysis in multiple aligned sequences of proteins).
• DIAMOD (Self-correcting distance geometry calculations of protein and DNA structures).
• NOAH (Structure-based automatic assignment of multidimensional NOESY spectra).
• PCPMer is a software tool for automatic motif detections of a protein family and identification of related family members in protein sequence database.
• InterProSurf is designed to predict the most likely sites on proteins to interact with other proteins, such as toxin elements, cell receptors and other proteins that make up virus capsids.
  

     Experimental/Model Structures from Our Group (Coming Soon!)

• Experimentally Determined Structures
  
• Computational Structures
  

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     Important Related Sites at UTMB

• Sealy Center for Structural Biology and Molecular Biophysics
• Computational Biology Computer Center Website
  
• Department of Biochemistry and Molecular Biology
  
• Sealy Center for Molecular Medicine
• Sealy Center for Vaccine Development
• Institute for Human Infections and Immunity
  
• National Institute of Environmental Health Sciences (NIEHS) Center in Environmental Toxicology
  
• Center for Biodefense and Emerging Infectious Diseases
• Department of Neuroscience and Cell Biology
  
• Department of Microbiology & Immunology
  
• Department of Pharmacology & Toxicology
  
• Department of Pathology
• Biophysical, Structural & Computational Biology
• Department of Cellular Physiology and Molecular Biophysics
• The NMR Research Facility at UTMB
• The UTMB Bioinformatics Service Core
  
• University of Texas Medical Branch

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Citations

'... One also should not forget the theoreticians. They are essential at virtually all forefronts of modern structural biology... It is apparent that a successful program in structural biology needs an environment in which a comfortable and effective interchange between the diverse practitioners is achieved.'

R.A. Lerner, The FASEB Journal, Vol.9 p.1, January 1995

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