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Group
Leaders
Dr.
Werner
Braun, Prof.
Dr.
Catherine Schein, Associate Prof.
Research
Homepage
Group Members
Ovidiu
Ivanciuc, Ph.D.
Surendra
Negi,
Ph.D.
Wenzhe Lu
Office
Assistant Page
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Welcome to the Computational Biology
Homepage!
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Former
Group Members
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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.
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Educational
Materials
- Computer
Modeling of Macromolecular Structure and
Function 2014 (Course Link
Available in January 2014)
- 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).
Braun Group Publications
Recent Group Presentations
Internal
Group Research Resource (Password
Protected)
Equipment
Documentation and Supplies (Password
Protected)
Group Library of Small Scripts and Programs
(Password
Protected)
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).
- 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.base.
- Flavitrack
contains over 475 complete genomic sequences from almost 40 different
flaviviruses, as well as related information on known mutations and
literature references. In addition, each sequence has been assigned a
unique identifier, i.e., a "license plate", which summarizes its date
and place of isolation, phenotype, and lethality. This enables us to
run very large sequence alignments and interpret the data with regard
to vector and symptom specificity within viral subclasses and strain
evolution.
- 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.
- EpiSearch
is designed to map conformational epitopes on a protein surface.
Please check back soon. The link to this program will be updated
once the corresponding manuscript has been published.
Experimental/Model
Structures from Our Group (Coming
Soon!)
- Experimentally Determined Structures
- Computational Structures
Important Related Sites at UTMB
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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