The following individuals contributed to the development of our web
resources and related research projects:
Present team members
Former team members
- Rafal Adamczak − SABLE, SIFT, MINNOU
- Frazier Baker − CoeViz
- Melanie Cushion − Pneumocystis Genome Project
- Jarek Meller − SABLE, MINNOU, CINTENY, POLYVIEW-2D/3D/MM, SCORPPION, SIFT, SPPIDER, Pneumocystis Genome Project, RLA and Protein disorder region prediction
- Alexey Porollo − POLYVIEW-2D/3D/MM/CoeViz, SABLE, MINNOU, SPPIDER, SCORPPION, Pneumocystis Genome Project, MutaCYP
- Michael Wagner − SABLE
Other precious contributors and consultants
- Jacek Biesiada − POLYVIEW-MM
- Baoqiang Cao − MINNOU
- Mirek Kordos − SCORPPION
- Mukta Phatak − RLA prediction
- Amit Sinha − CINTENY
- Bradley Slaven − Pneumocystis Genome Project
- Karthikeyan Swaminathan − Protein disorder region prediction
- Eric Martz − POLYVIEW-2D/3D/MM
- George Smulian − Pneumocystis Genome Project
We would like to thank Prakash Velayutham and his team for help in
resolving numerous technical issues during the
implementation of our projects. And we also would like
to thank all the users for their feedback that helped us
improve functionality of the web-servers.
We are very grateful to the authors of all software that is utilized by
our servers for making it available to the community and
graciously agreeing to incorporate it into public
W.L. DeLano's PyMol
from DeLano Scientific, San Carlos, CA, USA and
from Biomolecular Structures Group, Hertfordshire, UK
They are being used to render 3D images of macromolecular structures.
java applet by Jmol Development Team and Robert Hanson
It is being used for the quick protein structure lookups,
setting up specific view parameters, and trajectory visualization.
E. Martz's FirstGlance in Jmol server
from University of Massachusetts, Amherst, MA, USA
It is being used to identify contacts in
protein-ligand and protein-DNA/RNA complexes.
program by W. Kabsch and C. Sander
It is being used for calculation of protein
secondary structure and relative solvent accessibility from protein 3D coordinates.
program from National Center for Biotechnology Information (NCBI), USA
It is being used to perform sequence homology search
and obtain multiple sequence alignment.
server from L. Liang lab at University of Illinois at Chicago, USA
It is being used for finding pockets within
database from European Bioinformatics Institute
It is being used to find and map known protein
domains to the submitted structure.
database from the Institute of Enzymology, Budapest, Hungary
It is being used for mapping the protein regions
putatively spanning membrane to the submitted structure.
- Stuttgart Neural Network Simulator from University of
Stuttgart and University of Tübingen, Germany
It was used to build and train neural networks as part
of the systems for prediction of protein secondary structure,
relative solvent (or lipid) accessibility,
trans-membrane domains, and protein interaction sites.
- a Library for Support Vector Machines by C.-C. Chang
and C.-J. Lin from National Taiwan University, Taipei, Taiwan
It was used to build and train SVR-based models for
predicting relative solvent accessibility.
The FreeCSStemplates (now Templated)
- free CSS templates for web-design
One of their free templates was used to design the current look for our web-servers.
Some of their free charts are used for presenting the servers usage statistics.
Some of their modules are used to implement interactive analysis of protein residue coevolution.
Lincoln D. Stein's perl GD graphics library
that can be found at Boutell.Com, Inc. web server or
It is being used to generate images representing protein
sequence-structure-function 2D annotations and protein motion trajectories.
Nigel Brown's MView
from Central European Institute of Technology, Brno, Czech Republic
It is being used to visualize sequence alignments generated by PSI-BLAST.
This work has been partially supported by NIH grants
R01GM067823, R01AI055649, R24DK064403,
R21AI055338, R01AR050688, and P30ES006096.
We also gratefully acknowledge support
from the University of Cincinnati College of Medicine
and Cincinnati Children's Hospital Medical Center.