Bourne Laboratory - Publications

Last Update June 2008

2008

· A. Gramada and P.E.Bourne 2008 Resolving a Distribution of Charge into Multipole Moments of Minimum Magnitude: A Rankwise Distributed Multipole Expansion. Submitted.

· S.L Kinnings, N. Buchmeier, L. Xie and P.E. Bourne 2008 Discovery of novel drug leads to treat multi-drug and extensively drug resistant tuberculosis by repositioning safe pharmaceuticals: a chemical genomics approach with subsequent biological evaluation. Submitted.

· M. Corpas, N. Gehlenborg, S. Chandra Janga and P. E. Bourne 2008 Ten Simple Rules for Organizing a Scientific Meeting PLoS Comp. Biol. 4(5) e10000024. [PDF]

· S. Veretnik, C. Wills, P. Youkharibache, & P.E.Bourne 2008 Splicesome Genes Provide a Glimpse of Early Eukaryotic Evolution. J. Mol. Evol. Submitted.

· S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. (Perspective). Accepted.

· P.E.Bourne and L.M.Chalupa 2008 A New Approach to Scientific Dissemination Materials Today 11(6) 48 [PDF]

· R. Bauer, P.E. Bourne, A. Formella, C. Frömmel, G. Cornelius G. Christoph, G. Andrean, A. Aysam, A. Hoppe, E-W Knapp, T. Pöschel, B. Wittig, V. Ziegler, R. Preissner 2008 Superimposé: A 3D structural superposition server NAR 36(S2) W47-54 [PDF].

· J.L.Fink, S. Kushch, P. Williams & P.E.Bourne 2008 BioLit: Integrating Biological Literature with Databases NAR 36(S2) W385-389 [PDF].

· Q. Zhang, P. Wang, Y. Kim, P. Haste-Andersen, J. Beaver, P.E. Bourne, H-H. Bui, S. Buus, S. Frankild, J. Greenbaum, O. Lund, C. Lundegaard, M. Nielsen, J. Ponomarenko, A. Sette, Z. Zhu, B. Peters2008 Immune Epitope Database Analysis Resource (IEDB-AR) NAR. 36(S2) W513-W518[PDF]

· P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. (Editorial) 4(3) e1000037 [PDF].

· L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments. PNAS, 105(14) 5441-5446 [PDF].

· R. Valas and P.E. Bourne 2008 Rethinking Proteasome Evolution: Two Novel Bacterial Proteasomes. J. Mol. Evol. 66(5) 494-504 [PDF].

· K. Briedis, A. Starr and P.E. Bourne 2008 Analysis of the Human Kinome Using Methods Including Fold Recognition Reveals Two Novel Kinases PLoS ONE, 3(2): e1597. [PDF]

· J.G. Caporaso, N. Deshpande, J.L. Fink, P.E. Bourne, K.B. Cohen and L. Hunter 2008 Intrinsic Evaluation of Text Mining Systems May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing, 640-651. [PDF]

· S. Günther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E. Garcia Urdiales, A. Gewiess, L. Juhl Jensen, R. Schneider, R. Skoblo, R.B. Russell, P.E. Bourne, P. Bork and R. Preissner 2007 SuperTarget and Matador: Resources for exploring drug-target relationships NAR, 36:D919-922. [PDF]

2007

· J. Gu and P.E.Bourne 2007 Ten Simple Rules for Graduate Students. PLoS Comp. Biol. 3(11) e229. [PDF]

· L. Xie, J. Wang and P.E.Bourne 2007 In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators. PLoS Comp. Biol., 3(11) e217 [PDF].

· T.C. Erren, P. Cullen, M. Erren and P.E.Bourne 2007 Ten Simple Rules for Doing Your Best Research, According to Hamming PLoS Comp. Biol., 3(10): e213 [PDF]

· P.E. Bourne and S.E. Brenner 2007 Developing Computational Biology 3(9):e157 [PDF]

· J. Ponomarenko and P.E.Bourne 2007 Antibody-Protein Interactions: Benchmark Datasets and Prediction Tools Evaluation BMC Structural Biology 7(1):64 [HTML].

· J-L Chung, J. Beaver, E.D. Scheeff and P.E. Bourne 2007 Con-Struct Map: a Comparative Contact Map Analysis Tool Bioinformatics 23:2491-2492 [PDF].

· J.L. Fink and P.E.Bourne 2007 Reinventing Scholarly Communication for the Electronic Age. CT Watch, 3(3) 26-31 [HTML]

· H.M. Berman, K. Hendrick, H. Nakamura, J. Markley, P.E. Bourne, J. Westbrook (2007) Realism about PDB Nature Biotechnology, 25(8) 845-6. [PDF]

· L. Hunter, R.B.Altman and P.E. Bourne 2007 The International Society for Computational Biology 10^th Anniversary PLoS Comp. Biol. 3(6) e135 [PDF]

· J-L Chung, W Wang and P.E.Bourne 2007 High-throughput identification of Interacting Protein-Protein Binding Sites. BMC Bioinformatics, 8(1): 223 [PDF].

· L. Xie and P.E. Bourne 2007 A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites BMC Bioinformatics, 8(Suppl 4):S9 [PDF].

· P.E. Bourne 2007 Ten Simple Rules for Making Good Oral Presentations, PLoS Comp. Biol., 3(4)e77 [PDF].

· J.E Beaver, P.E Bourne and J.V Ponomarenko 2007 EpitopeViewer: a Java Application for the Visualization and Analysis of Immune Epitopes in the IEDB database. Immunome Research, 3(1):3 [PDF].

· Q. Vicens and P.E.Bourne 2007 Ten Simple Rules for Collaboration PLoS Comp. Biol., 3(3) e44 [PDF].

· P.E. Bourne and A. Godzik 2007 Structural Genomics in Bioinformatics – From Genomes to Therapies T. Lengauer (Ed.) Wiley-VCH. p419-438. [PDF]

· J. Gu and P.E.Bourne 2007 Allosteric Fluctuation Transitions as Applied to Cyclin Dependent Kinase 2 BMC Bioinformatics 8(1):45. [PDF]

2006

· P Guda, P.E. Bourne and C. Guda 2006 Conserved Motifs in Voltahge-sensing and Pore-forming Modules of Voltage-gated Ion Channel Proteins Biochem. Biophys. Res. Com. 352(2) 292-8 [PDF].

· P.E. Bourne and I. Friedberg 2006 Ten Simple Rules for Getting a Post Doc. PLoS Comp. Biol., (Editorial), 2(11) e121. [PDF]

· A.Sette, H.H.Bui, J.Sidney, P.E.Bourne, S. Buus, W. Fleri, R.Kubo, O.Lund, D.Nemazee, J.V.Ponomarenko, M.Sathiamurthy, S. Stweart, S.Way, S.S.Wilson and B. Peters 2006 The Immune Epitope Database and Analysis Resource Pattern Recognition in Bioinformatics, Springer, Jagath C. Rajapakse, Limsoon Wong, Raj Acharya
(Eds) [PDF]

· C.L. Dupont, S.Yang, B. Palenik and P.E.Bourne 2006 Putative Imprints in Modern Proteomes of Ancient Shifts in Trace Metal Geochemistry PNAS, 103(47) 17822-17827 [PDF].

· P.E.Bourne and J. McEntyre 2006 Biocurators: Contributors to the World of Science PLoS Comp. Biol., (Editorial) 2(10) e142 [PDF].

· E.D Scheeff and P.E. Bourne 2006 Application of Protein Structure Alignments to Iterated Hidden Markov Model Protocols for Structure Prediction. BMC Bioinformatics, 7:410 [html].

· H.M. Berman,S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack, Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann,D. Jones,J.L. Markley, John Moult, G.T. Montelione, C. Orengo, M.G. Rossmann,B. Rost,²¹ H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook2006 Acrhiving Structural Models of Biological Macromolecules. Structure, 14:1211-1217. [PDF]

· P.E.Bourne and A. Korngreen 2006 Ten Simple Rules for Reviewers. PLoS Comp. Biol., (Editorial), 2(9) e110 [HTML]

· P.E.Bourne 2006 One Year of PLoS Computational Biology PLoS Comp. Biol., (Editorial) 2(8):e111. [PDF]

· P.E. Bourne and S. Brunak 2006 ISMB 2006 (Editorial) Bioinformatics 22(14):e1-2 [PDF]

· R. Vita, K. Vaughan, L. Zarebski, N. Salimi, W. Fleri, H. Grey, M. Sathiamurthy, J. Mokili, H-H. Bui, P.E Bourne, J. Ponomarenko, R. DE Castro Jr, R.K Chan, J. Sidney, S.S Wilson, S. Stewart, S. Way, B. Peters and A. Sette 2006 Curation of Complex, Content-dependant Immunological Data BMC Bioinformatics, 7(1), 341 [HTML]

· J. Gu, M. Gribskov and P.E. Bourne 2006 Wiggle – Predicting Functionally Flexible Regions from Primary Sequence PLoS Comp. Biol., 2(7) e90. [PDF]

· T. Holland, S. Veretnik, I.N. Shindyalov, P.E. Bourne 2006 A Benchmark for Domain Assignment from Protein 3-dimensional Structure and it’s Applications J. Mol. Biol., 361(3), 562-590. [HTML].

· A. Gramada and P.E. Bourne 2006 Multipolar Representation of Protein Structure BMC Bioinformatics, 7:242 [HTML].

· J-L Chung, W. Wang and P.E. Bourne 2006 Exploiting Sequence and Structure Homology to Identify Protein-Protein Binding Sites Proteins: Structure, Function and Bioinformatics 62(3) 630-640. [PDF].

· P.E.Bourne and L.M.Chalupa 2006 Ten Simple Rules for Getting a Grant PLoS Comp. Biol., (Editorial) 2(2) e12 [pdf].

· A. Kouranov,L. Xie, J. de la Cruz, L. Chen, J. Westbrook,P.E. Bourne and H.M. Berman 2006 The RCSB PDB Information Portal for Structural Genomics Nucleic Acids Research, 34 D302-5. [HTML]

2005.

· E. Scheeff and P.E. Bourne 2005 Structural Evolution of the Protein Kinase-Like Superfamily PLoS Comp. Biol. 1(5): e49. [open access]

· P.E. Bourne, W.F. Bluhm, N. Deshpande, Q. Zhang, K. Burkhardt, H.M. Berman, J.L. Flippen-Anderson 2005 The Protein Data Bank. The Encyclopedia of Medicinal Chemistry Accepted.

· P.E. Bourne 2005 Ten Simple Rules for Getting Published PLoS Comp. Biol. 1(5) e57. [open access]

· M. Sathiamurthy, B. Peters, H. Bui, J. Sidney, J.Mokili, S.S. Wilson, W. Fleri, D.L. McGuinness, P.E. Bourne and A. Sette 2005 An Ontology for Immune Epitopes: Application to the Design of a Broad Scope Database of Immune Reactivities Immunome Research 1:2 [Open Access]

· P.E. Bourne 2005 In the Future will a Biological Database Really be Different from a Biological Journal? PLoS Comp. Biol. 1(3) e34 [PDF]

· P.M.D. Fitzgerald, J. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman 2003 The Macromolecular Crystallographic Information File (mmCIF) The International Tables for X-ray Crystallography Volume G. In Press. [PDF]

· L. Xie and P.E. Bourne 2005 Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets and Homology Models. PLoS Comp Biol 1(3) e31. [PDF]

· B. Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M. Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S. Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Design and Implementation of the Immune Epitope Data Base and Analysis Resource Immunogenetics. 57(5): 326-36 [PDF]

· P.E. Bourne, S.E. Brenner, M.B. Eisen (2005) PLoS Computational Biology: A New Community Journal. PLoS Comp Biol 1(1): e4 [HTML]

· B. Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M. Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S. Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Immune Epitope Database and Analysis Resource: From Vision to Blueprint. PLoS Biology, 3(3) e91. [PDF]

· Shahab, A., Chuon, D., Suzumura, T., Li, W. W., Byrnes, R. W.,Tanaka, K., Ang, L., Matsuoka, S., Bourne, P. E., Miller, M. A. & Arzberger, P. W. 2005. Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. Lecture Notes In Computer Science, 3370:53-67. [PDF]

· Birnbaum, A., Hayes, J., Li, W. W., Miller, M. A., Arzberger, P.W., Bourne, P. E. & Casanova, H. 2005. Grid Workflow Software for High-Throughput Proteome Annotation Pipeline. Lecture Notes In Computer Science, 3370: 68-61. [PDF]

· J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne 2005 The Molecular Biology Toolkit (mbt): A Modular Platform for Developing Molecular Visualization Applications. BMC Bioinformatics, 6:21. [PDF] [Open Access]

· J.V. Ponomarenko, P.E. Bourne and I.N. Shindyalov 2005 Assigning New GO Annotations to Protein Data Bank Sequences by Structural Homology Proteins: Structure, Function and Bioinformatics 58: 855-865. [PDF]

· Q. Zhang, S. Veretnik and P.E.Bourne 2005 Structural Bioinformatics in Bioinformatics Technologies, pp. 15-40, Ed. Y-P.P. Chen, Springer-Verlag, Berlin.

S. Yang, R.F. Doolittle and P.E. Bourne 2005 Phylogeny Determined through Protein Domain Content Proc. Nat. Acad. Sci. (USA) 102(2): 373-378. [PDF] [Supplimental Material] [Editor’s choice Science]

N. Deshpande,K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W.Townsend-Merino, Q. Zhang, C. Knezevich, L. Chen, Z. Feng, R. Kramer Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Bermanand P.E. Bourne 2005 The RCSB Protein Data Bank: A Redesigned Query System and Relational Database Based on the mmCIF Schema Nucleic Acids Research. 33: D233-D237. [PDF]
PC Babbitt, PE Bourne, SD Mooney 2005 Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pacific Symposium on Biocomputing 319-321. [PDF]

2004

P.E.Bourne 2004. Protein Resources in Encyclopedia of Biological Chemistry, Eds W.J. Lennarz & M.D. Lane, Elsevier, Oxford, Vol. 3 pp 478-483.
Li, W. W., Byrnes, R. W., Hayes, J., Birnbaum, A., Reyes, V. M., Shahab,A., Mosley, C., Pekurovsky, D., Quinn, G. B., Shindyalov, I. N., Casanova, H., Ang, L., Berman, F., Arzberger, P. W., Miller, M. A. & Bourne, P. E. 2004. The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Computing, 22: 127-136.
Y. Jia, G.T. Dewey, I.N. Shindyalov and P.E. Bourne2004 A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. J. Comp. Biol. 11(5) 787-799. [PDF]
W.G Krebs and P.E. Bourne 2004 Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinformatics and Computational Biology, 2(1) 61-75. [PDF]
C. Guda, S. Lu, E.D. Scheeff, P.E. Bourneand I.N. Shindyalov 2004 CE-MC: A multiple protein structure alignment server. Nucleic Acids Research, 32 W100-W103. [PDF]
S. Verentik, P.E. Bourne, N.N. Alexandrov, I.N. Shindyalov 2004. Towards consistent assignment of structural domains in proteins. Journal of Molecular Biology, 339(3), 647-678 [PDF].
D. Pekurovsky, I.N. Shindyalov, P.E. Bourne 2004 High Throughput Biological Data Processing on Massively Parallel Computers. A Case Study of Pairwise Structure Comparison and Alignment Using the Combinatorial Extension (CE) Algorithm. Bioinformatics, 20(12) 1940-1947 [PDF].
P.E. Bourne, J. Westbrook and H.M. Berman 2004. The Protein Data Bank and Lessons Learned in Data Management. Briefings in Bioinformatics. 5(1), 23-30. [PDF]
W.G. Krebs and P.E. Bourne 2004 Statistically Rigorous Automated Protein Annotation Bioinformatics 10(7) 1066-1073 [PDF]
H.M. Berman, P.E. Bourne and J. Westbrook 2004 The Protein Data Bank: A Case Study in the Management of Community Data. Current Proteomics 1, 49-57. [PDF]
P.E. Bourne, K.J. Addess, W.F. Bluhm, L. Chen, N. Deshpande, Z. Feng³, R. Kramer Green, J. C. Merino-Ott, W. Townsend-Merino, H. Weissig, J. Westbrook, H. M. Berman 2004. The Distribution and Query Systems of the RCSB Protein Data Bank Nucleic Acids Research, 32, D223-225 [PDF]

P.E. Bourne, C.K.J. Allerston,W. Krebs, W. Li, I.N Shindyalov, A. Godzik, I. Friedberg, T. Liu, D. Wild, S. Hwang, Z. Ghahramani L. Chen, and J. Westbrook 2004. The Status of Structural Genomics through the analysis of current targets and structures. 2004 Pacific Symposium on Biocomputing 404-416. [html]

2003

P.E. Bourne 2003 The Status of Structural Genomics Targets 2(5) 181-1182 (Editorial). [PDF]

W.G Krebs and P.E. Bourne 2003 Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. Proceedings of the 2003 IEEE Computer Society Bioinformatics Conference Proceedings 180-189 [PDF]..
W.W. Li¹, G.B. Quinn, N. N. Alexandrov, P.E. Bourne and I.N. Shindyalov 2003 Proteins of Arabidopsis thaliana (PAT) database: A resource for comparative proteomics Genome Biology 4(8), R51 [PDF]

K.S. Doctor, J. Reed, A. Godzik and P.E.Bourne 2003 The Apoptosis Database Cell Death and Differentiation 10(6), 621-633. [PDF]

P. Yang, P.A. Craig, D. Goodsell and P.E. Bourne 2003 BioEditor - Simplifying Macromolecular Structure Annotation Bioinformatics 19(7) 897-898. [PDF]

P.E.Bourne 2003 Free access to publicly funded databases is vital Nature 421, 786 [PDF]

H.M. Berman, P.E. Bourne, J.D. Westbrook and C. Zardecki 2003 The Protein Data Bank pp 389-406 from Structure (ed.) Chasman Marcel Decker Inc. NY.

K. Baldridge and P.E. Bourne 2003 The New Biology and the Grid. Chapter 40 pp 907-922 from Grid Computing - Making the Global Infrastructure a Reality (eds) F.Berman, G. Fox and T.Hey Wiley, New York.

2002

J.V. Ponaramenko, I.N. Shindyalov and P.E. Bourne 2002 Building an Automated Classification of DNA-binding Protein Domains Bioinformatics 18:S192-201.[pdf]
P Craig, P Yang and PE Bourne 2002 BioEditor A Tool for Structure Annotation FASEB J 16 (5): A741-A742.
P.E. Bourne 2002 Science's Policy on Data Deposition. Science 296, 1609 (Letter)
I.N. Shindyalov and P.E. Bourne 2002 New Insights into Protein Fold Space and Sequence-Structure Relationships. Structure Prediction:Bioinformtic Approach, Chapter 17, pp 417-428, Ed. I. Tsigelny. Int'l University Line, La Jolla, CA.
Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, and Ilya N. Shindyalov 2002, Comparative Analysis of Protein Structure: New Concepts and Approaches for Multiple Structure Alignment. Structure Prediction:Bioinformtic Approach. Chapter 19, pp 449-459. Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
Eric D. Scheeff, Philip E. Bourne, and Ilya N. Shindyalov 2002 Comparative Analysis of Protein Structure: Automated vs. Manual Alignment of the Protein Kinase Family. Protein Structure Prediction:Bioinformtic Approach, Chapter 20, pp 463-475. Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
H.M. Berman, T. Battistuz, T.N.Bhat, W.F. Bluhm, P.E. Bourne, K. Burkhardt, Z. Feng, G.L. Gilliland, L. Iype, S. Jain, P. Fagan, J. Marvin, V. Ravichandran, B. Schneider, N. Thanki, D. Padilla, H. Weissig, J.D. Westbrook, C. Zardecki 2002 The Protein Data Bank Acta Cryst. D58, 899-907. [pdf]
I.N. Shindyalov and P.E. Bourne 2002 Structure Structure Comparison and Alignment Structural Bioinformatics Chapter 16 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
H. Wessig and P.E. Bourne 2002 Other Structure Based Databases Structural Bioinformatics Chapter 11 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
B.V.B Reddy and P.E. Bourne 2002 A User's Perspective on the Structure Classification of Proteins (SCOP) Structural Bioinformatics Chapter 12 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
H.M. Berman, D. Goodsell and P.E. Bourne 2002 Proteins Sturctures: From Famine to Feast American Scientist 90: 350-359. [synopsis] [Full PDF]
DS. Greer, JD. Westbrook and PE. Bourne 2002 An Ontology Driven Architecture for Derived Representations of Macromolecular Structure Bioinformatics 18: 1280-128 [pdf].
BVB Reddy, W. Li, and P.E.Bourne 2002 Conserved Key Amino Acid Positions Used to Morph Protein Folds Biopolymers 64(3):139-145. [pdf]
H.Weissig and P.E. Bourne 2002 Macromolecular Structure Databases Acta Cryst. D 58(6) 908-915. [pdf]
A. Kuller, W. Fleri, W.F. Bluhm, J.L. Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to Synchrotron Resources TIBS 27(4):213-215 [pdf].
J. Westbrook, Z.Feng, S. Jain, T.N.Bhat, N. Thanki, V.Ravichandran, G.L.Gilliland, W.Bluhm, H. Weissig, D.S.Greer, P.E.Bourne, and H.M.Berman 2002 The Protein Data Bank: Unifying the Archive. Nucleic Acids Research, 30:245-248. [pdf]
W. Li, BVB Reddy, J. Tate, IN Shindyalov and P.E.Bourne 2002 CKAAPs DB: A Conserved Key Amino Acid Positions Database. Nucleic Acids Research 30: 409-411. [pdf]

2001

D.Greer, J. Westbrook, and P.E.Bourne 2001 OpenMMS: An Ontology Driven Architecture for Macromolecular Structure Objects in Bio- and Chem-informatics (OIBC)
A. Kuller, W. Fleri, W.F. Bluhm, J.L. Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to Synchrotron Resources Nature Structure Biology 8(8) 663.
I.N.Shindyalov and P.E.Bourne 2001 Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’01). The Sequence-Structure Space and Data Redundancy in the Protein Data Bank. 139-145.
D.S. Greer, J. Westbrook, P.E. Bourne 2001 Proceedings NETTAB - Network Tools and Applications in Biology

CORBA and XML: Towards a Bioinformatics Integrated Network Environment. An Ontology Driven Architecture for Macromolecular Structure.

J.G. Tate, J. Moreland, and P.E. Bourne 2001 J. Mol. Graphics 19, 280-287. Design and Implementation of of a Collaborative Molecular Graphics Environment.[PDF file]
B.V.B Reddy, W. Li, I.N. Shindyalov, and P.E. Bourne 2001 Proteins: Structure, Function and Genetics 42(2) 148-163. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. [PDF file]
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne 2001 International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules Rossmann, M.G. and Arnold, E. Editors Dordrecht: Kluwer Academic Publishers, The Netherlands pp. 675-681. The Protein Data Bank 1999-.
W.W.Li, B.V.B. Reddy, I.N. Shindyalov and P.E. Bourne 2001 Nucleic Acid Research, 29(1) 329-331. CKAAPs DB: A Conserved Key Amino Acid Position Database. [PDF file]