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Protein Data Bank in Europe : Publications

Following is a list of peer-reviewed publications involving the PDBe staff. Additional list available here. The Article title (with a CiteXplore link), Journal name, and the name of PDBe members involved are listed.

2010 2009 2008 2007 2006 2005 2004 2003 2002 2000 1999 1998

2010
Safeguarding the integrity of protein archive. Nature - Kleywegt GJ et al.
Crystal contacts as nature's docking solutions. J Comput Chem - Krissinel EB

2009
PDBe: Protein Data Bank in Europe. Nucleic Acids Res. - Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ et al. (Download PDF)
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J Biomol NMR - Vranken WF, Penkett CJ et al. (Download PDF)
The Worldwide Protein Data Bank. Structural Bioinformatics, Chp. 11 (ISBN: 978-0-470-18105-8) - Henrick, K et al.
Applications of Graph Theory in Chemo- and Bioinformatics. Analysis of Complex Networks, pp. 221-244 (ISBN: 978-3-527-32345-6) - Dimitropoulos D, Golovin A, John M, Krissinel E
CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods - Vranken WF et al.
A chemogenomics view on protein-ligand spaces. BMC Bioinformatics - Kleywegt GJ et al. (Download PDF)
Relationship between chemical shift value and accessible surface area for all amino acid atoms. BMC Struct Biol. - Vranken WF et al. (Download PDF)
Case-controlled structure validation. Acta Crystallogr D Biol Crystallogr. - Kleywegt GJ et al. (Download PDF)
On vital aid: the why, what and how of validation. Acta Crystallogr D Biol Crystallogr. - Kleywegt GJ (Download PDF)
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol. - Swaminathan GJ, Henrick K et al.
COCO: a simple tool to enrich the representation of conformational variability in NMR structures. Proteins - Vranken W et al.

2008
Chemical substructure search in SQL. J Chem Inf Model.- Golovin A, Henrick K et al.
Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space. J Chem Inf Model. - Kleywegt GJ et al.
MSDmotif: exploring protein sites and motifs. BMC Bioinformatics - Golovin A, Henrick K et al. (Download PDF)
Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov Today - Kleywegt GJ et al.
An alternative method for the evaluation of docking performance: RSR vs RMSD. J Chem Inf Model. - Kleywegt GJ et al.
Remediation of the protein data bank archive. Nucleic Acids Res.- Henrick K, Dimitropoulos D, Ionides J, Krissinel E, Newman R, Swaminathan J, Velankar S, Vranken W et al. (Download PDF)
Data deposition and annotation at the worldwide protein data bank. Methods Mol. Biol.- Swaminathan GJ, Henrick K et al.

2007
Problems of protein three-dimensional structures. Comprehensive Medicinal Chemistry II, Vol 3, pp. 531-550 (ISBN: 978-0-08-044513-7) - Swaminathan GJ et.al.
A global analysis of NMR distance constraints from the PDB. J Biomol NMR - Vranken W (Download PDF)
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res.- Henrick K et al. (Download PDF)

2006
A nomenclature and data model to describe NMR experiments. J Biomol NMR - Vranken W et al.
SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. - Pajon A, Rachedi A, Vranken W, Whamond G, Henrick K et al. (Download PDF)
Outcome of a workshop on archiving structural models of biological macromolecules. Structure - Henrick K et al.
E-MSD: improving data deposition and structure quality. Nucleic Acids Res. - Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S. (Download PDF)

2005
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J Biomol NMR. - Vranken W et al.
RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins - Vranken W et al.
The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins - Vranken WF, Pajon, A, Ionides J et al.
The Protein Data Bank (PDB) and the World Wide PDB Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics: vol 7, pp. 3335-3339. (ISBN: 978-0-470-84974-3) - Henrick K et al.
Multiple Alignment of Protein Structures in Three Dimensions. Computational Life Sciences: pp. 67-78. (ISBN: 978-3-540-29104-6) - Krissinel E, Henrick K
Detection of Protein Assemblies in Crystals. Computational Life Sciences: pp. 67-78. (ISBN: 978-3-540-29104-6) - Krissinel E, Henrick K
Cation-pi interactions in protein-protein interfaces. Proteins - Golovin A et al.
A framework for scientific data modeling and automated software development. Bioinformatics - Vranken WF, Pajon A, Ionides JM et al. (Download PDF)
RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics - McNeil P et al. (Download PDF)
PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics - Henrick K et al. (Download PDF)
E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res. - Velankar S, McNeil P, Suarez A, Henrick K et al. (Download PDF)
Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins - Pajon A, Ionides J, Vranken W, Henrick K et al.
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins - Golovin A, Dimitropoulos D, Oldfield T, Rachedi A, Henrick K

2004
Unconventional interactions between water and heterocyclic nitrogens in protein structures. Proteins - Velankar S, Golovin A et al.
DRESS: a database of REfined solution NMR structures. Proteins - Vranken W et al.
Common subgraph isomorphism detection by backtracking search. Software - Practics and Experience - Krissinel E, Henrick K
Issues in the Annotation of Protein Structures. Database Annotation in Molecular Biology: Principles and Practice (ISBN: 0-470-85681-5) - Henrick K, Hussain A, Ionides J, Newman R, Swaminathan J, Tate J, Velankar S
The European Bioinformatics Institute Macromolecular Structure Relational Database Technology. Database Annotation in Molecular Biology: Principles and Practice (ISBN: 0-470-85681-5) - Boutselakis H, Dimitropoulos D, Henrick K, Ionides J, John M, Keller PA, McNeil P, Pineda J, Suarez-Uruena A
E-MSD: an integrated data resource for bioinformatics. - Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K (Download PDF)
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. - Krissinel E, Henrick K (Download PDF)
The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography. Acta Crystallogr D Biol Crystallogr. - Krissinel E et al. (Download PDF)
Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr. - Krissinel E et al. (Download PDF)
A Java applet for multiple linked visualization of protein structure and sequence. J Comput Aided Mol Des. - Oldfield TJ

2003
EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J Struct Biol. - Henrick K, Newman R, Tagari M et al.
Announcing the worldwide Protein Data Bank. Nat Struct Biol. - Henrick K et al.
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure - Kleywegt GJ, Henrick K et al.
A structure-based anatomy of the E.coli metabolome. J Mol Biol. - Krissinel EB et al.
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res. - Boutselakis H, Dimitropoulos D, Fillon J, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W (Download PDF)
The European Bioinformatics Institute's data resources. Nucleic Acids Res. - Henrick K et al. (Download PDF)
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins - Henrick K et al.
The European Bioinformatics Institute Macromolecular Structure Database (E-MSD) Protein Structure: Determination, Analysis, and Applications for Drug Discovery (ISBN: 9780824740320) - Dimitropoulos D, Keller P, Henrick K, Ionides J, Krissinel E, McNeil P, Velankar S

2002
The CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr. - Krissinel E et al.
New electron microscopy database and deposition system. Trends Biochem Sci. - Tagari M, Newman R, Henrick K et al.
The CCPN project: an interim report on a data model for the NMR community. Nat Struct Biol. - Vranken WF, Pajon A, Ionides JM et al.
VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. J Cell Biol. - Newman R et al.
Sequential SNARE disassembly and GATE-16-GOS-28 complex assembly mediated by distinct NSF activities drives Golgi membrane fusion. J Cell Biol. - Newman R et al.

2000
Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins - Henrick K et al.
Molecular modeling and mutagenesis studies of the N-terminal domains of galectin-3: evidence for participation with the C-terminal carbohydrate recognition domain in oligosaccharide binding. Glycobiology - Henrick K et al.

1999
Report from the Joint CCP4/EBI Software Developers and Data Harvesting Workshop CCP4 Newsletter on protein crystallography - Henrick K et al.

1998
Evidence for subsites in the galectins involved in sugar binding at the nonreducing end of the central galactose of oligosaccharide ligands: sequence analysis, homology modeling and mutagenesis studies of hamster galectin-3. Glycobiology - Henrick K et al.
PQS: a protein quaternary structure file server. Trends Biochem Sci. - Henrick K et al.
Crystal structure of phosphate binding protein labeled with a coumarin fluorophore, a probe for inorganic phosphate. Biochemistry - Henrick K et al.
Deposition of macromolecular structures. Acta Crystallogr D Biol Crystallogr. - Keller PA, Henrick K, McNeil P, Barton GJ et al.
CCP4 and Data Harvesting CCP4 Newsletter on protein crystallography - Henrick K

Publications archive managed by: Gaurav Sahni

Page last updated: 21-JAN-2010