BioCoRE: A Collaboratory for Structural Biology Milind Bhandarkar 1,2 , Gila Budescu 2 , William F. Humphrey 5 , Jesus A. Izaguirre 1,2 , Sergei Izrailev 2,3 , Laxmikant V. Kale 1,2 , Dorina Kosztin 2,4 , Ferenc Molnar 2 , James C. Phillips 2,3 , and Klaus Schulten 2,3 1 Department of Computer Science, 2 Beckman Institute, and Departments of 3 Physics and 4 Chemistry University of Illinois at Urbana-Champaign, Urbana, IL 61801 5 Advanced Computing Lab Los Alamos National Laboratory Los Alamos, NM 87545 email: kschulte@ks.uiuc.edu Biology, Network, Software Engineering, Interactive Simulation, Collaboratory ABSTRACT Modern computational structural biology requires scientists to employ a wide range of tools and tech- niques to solve complex problems while keeping ac- curate records of research activities. Additional com- plications are introduced by the need to effectively engage in interdisciplinary collaborations with geo- graphically dispersed colleagues. The software Bio- CoRE,acollaborativeresearchenvironmentformole- cular modeling and simulations, addresses these chal- lenges. Initial design work has led to a web-based architecture focused on four primary interface par- adigms: a workbench allows diverse computational tools to be applied to the problem at hand in a consistent manner, a notebook automates record- ing of research activities, electronic conferences held with collaborators can be saved and replayed, and multi-author documents can be prepared in a cross- platform revision control system. When complete, it is expected that the BioCoRE meta-application will drastically reduce the effort and expense presently associated with structural biology distance collabo- rations. INTRODUCTION Structural biology investigates the molecular ba- sis of life in its healthy and diseased states. Initially through x-ray diffraction (Perutz et al., 1960; Kendrew et al., 1960), later through NMR (Wuethrich, 1986), and lately also through electron microscopy (Nogales et al., 1998), ever more medically relevant and larger biomolecular structures have been discovered. The blossoming field of genomics rivals structural biology with an outpouring of genomes. The vast amount of information available and the complex- ity of the information units, gene sequences and pro- tein structures, have made computers indispensable tools in biomedical research to an extent which in 1991 was characterized as a paradigm shift by W. Gilbert (Gilbert, 1991). Today about 200 differ- ent programs serve researchers well, in particular those coupled with web-based tools such as the Bi- ology Workbench * , PROPSEARCH † (Hobohm and Sander, 1995), and BLAST ‡ (Altschul et al., 1990). Programs for structural biology have been mostly single-user oriented and not integrated with web- based tools. Here we suggest to develop a “Bio- logical Collaborative Research Environment” (Bio- CoRE), an integrated, web-based, and tool-oriented * URL: http://biology.ncsa.uiuc.edu/ † URL: http://www.embl-heidelberg.de/prs.html ‡ URL: http://www.ncbi.nlm.nih.gov/BLAST/