Acknowledgements

The following individuals contributed to the development of our web resources and related research projects:

Present 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

Former team members

• 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

Other precious contributors and consultants

• 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 domain servers.

• W.L. DeLano's PyMol from DeLano Scientific, San Carlos, CA, USA and
  Roger Sayle's RasMol from Biomolecular Structures Group, Hertfordshire, UK
  They are being used to render 3D images of macromolecular structures.
• The Jmol 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.
• The DSSP 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.
• The BLAST program from National Center for Biotechnology Information (NCBI), USA
  It is being used to perform sequence homology search and obtain multiple sequence alignment.
• The CASTp server from L. Liang lab at University of Illinois at Chicago, USA
  It is being used for finding pockets within macromolecular structure.
• The Pfam database from European Bioinformatics Institute
  It is being used to find and map known protein domains to the submitted structure.
• The PDBTM database from the Institute of Enzymology, Budapest, Hungary
  It is being used for mapping the protein regions putatively spanning membrane to the submitted structure.
• SNNS - 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.
• LibSVM - 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.
• The FusionCharts - flash- and javascript-based charts
  Some of their free charts are used for presenting the servers usage statistics.
• D3 and Aight Javascript libraries
  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 CPAN.
  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.