Helen Berman
Professor

Director. Protein Data Bank
Rutgers University
Department of Chemistry
610 Taylor Road. Wright Lab
Rutgers University
Piscataway. N. J. 08854
(732) 445-4667. FAX - 4320
berman@rcsb.rutgers.edu

Nucleic acid and protein structure. crystallography. biological databases

Our goal is to understand the structural properties of biological molecules and to relate these structures to their biological functions. Our work on nucleic acids has focused on the effects of base modification of the structure and on the interrelationships of hydration structure. crystal packing. and conformation. Our studies of DNA-protein complexes will help to elucidate the principles that underlie interactions between these macromolecules. Studies on collagen peptides have allowed us to define the structure of the triple helix at atomic resolution and to understand the role of water in mediating intermolecular interactions.

Protein Data Bank (PDB; http://www.rcsb.org/pdb/)

The PDB is the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

Research Collaboratory for Structural Bioinformatics (http://www.rcsb.org/)

The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium dedicated to improving our understanding of the function of biological systems through an understanding of 3-dimensional biological macromolecular structure.

Nucleic Acid Database (http://ndbserver.rutgers.edu/)

We have continued the development of a relational database of three dimensional structures of nucleic acids and their constituents. The database has been expanded to include protein-nucleic acid complexes. A wide variety of reports can be created. including tables and graphs of structural and statistical information about nucleic acids. An electronic newsletter is published on a bimonthly basis and is sent to users around the world. We have developed a forms based interface that allows for simple queries using the World Wide Web. We have also developed a dictionary of the standard geometry of nucleic acids which is used by this project to validate structures and has been incorporated into X-PLOR.

Selected Publications

Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H. (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR. 40(3):153-5.

Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM (2008); RNA Ontology Consortium. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
RNA. 14(3):465-81.

Berman HM. (2008) Harnessing knowledge from structural genomics. Structure. 16(1):16-8.

Berman HM. (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr A. 64(Pt 1):88-95.

Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. (2008) Remediation of the protein data bank archive.
Nucleic Acids Res. 36(Database issue):D426-33.

Berman HM, Henrick K, Nakamura H, Markley J, Bourne PE, Westbrook J. (2007) Realism about PDB. Nat Biotechnol. 25(8):845-6.

Berman H, Henrick K, Nakamura H, Markley JL. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. Jan;35(Database issue):D301-3.

Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL Jr, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 14(8):1211-7.

Bella J, Liu J, Kramer R, Brodsky B, Berman HM. (2006) Conformational effects of Gly-X-Gly interruptions in the collagen triple helix. J Mol Biol. 362(2):298-311.

Leontis NB. Altman RB. Berman HM. Brenner SE. Brown JW. Engelke DR. Harvey SC. Holbrook SR. Jossinet F. Lewis SE. Major F. Mathews DH. Richardson JS. Williamson JR. Westhof E. R (2006) The RNA Ontology Consortium: an open invitation to the RNA community. RNA. 12(4):533-41.

Napoli AA. Lawson CL. Ebright RH. Berman HM. (2006) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J Mol Biol. 357(1):173-83.

Kouranov A. Xie L. de la Cruz J. Chen L. Westbrook J. Bourne PE. Berman HM. (2006) The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 34(Database issue):D302-5.

Dutta S. Berman HM. (2005) Large macromolecular complexes in the Protein Data Bank: a status report. Structure. 13(3):381-8.

McLaughlin WA. Kulp DW. de la Cruz J. Lu XJ. Lawson CL. Berman HM. (2004) A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. J Struct Funct Genomics. 5(4):255-65.

Berman HM. Ten Eyck LF. Goodsell DS. Haste NM. Kornev A. Taylor SS. (2005) The cAMP binding domain: an ancient signaling module. Proc Natl Acad Sci U S A. 102(1):45-50. Epub 2004 Dec 23.

Deshpande N. Addess KJ. Bluhm WF. Merino-Ott JC. Townsend-Merino W. Zhang Q. Knezevich C. Xie L. Chen L. Feng Z. Green RK. Flippen-Anderson JL. Westbrook J. Berman HM. Bourne PE. (2005) The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.
Nucleic Acids Res. 33(Database issue):D233-7.

Pajon A. Ionides J. Diprose J. Fillon J. Fogh R. Ashton AW. Berman H. Boucher W. Cygler M. Deleury E. Esnouf R. Janin J. Kim R. Krimm I. Lawson CL. Oeuillet E. Poupon A. Raymond S. Stevens T. van Tilbeurgh H. Westbrook J. Wood P. Ulrich E. Vranken W. Xueli L. Laue E. Stuart DI. Henrick K. (2005) Design of a data model for developing laboratory information management and analysis systems for protein production.
Proteins. 58(2):278-84.

Westbrook J. Ito N. Nakamura H. Henrick K. Berman HM. (2005) PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics. 21(7):988-92.

Yang H. Guranovic V. Dutta S. Feng Z. Berman HM. Westbrook JD. (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 60(Pt 10):1833-9.

Berman HM. Westbrook JD. (2004) The impact of structural genomics on the protein data bank.
Am J Pharmacogenomics. 4(4):247-52.

Lawson CL. Benoff B. Berger T. Berman HM. Carey J.(2004) E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure. 12(6):1099-108.

Bourne PE. Westbrook J. Berman HM. (2004) The Protein Data Bank and lessons in data management.
Brief Bioinform. 5(1):23-30.

Chen L. Oughtred R. Berman HM. Westbrook J. (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics. 20(16):2860-2.

Lawson CL. Swigon D. Murakami KS. Darst SA. Berman HM. Ebright RH. (2004) Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol. 14(1):10-20.

Feng Z. Chen L. Maddula H. Akcan O. Oughtred R. Berman HM. Westbrook J. (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics. 20(13):2153-5.

Schneider B. Moravek Z. Berman HM. (2004) RNA conformational classes. Nucleic Acids Res. Mar 11;32(5):1666-77.

McLaughlin. WA and Berman. HM (2003) Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J. Mol. Biol. 330:43-55.

Neidle. S. Schneider. B. Berman. HM (2003). Fundamentals of DNA and RNA structure. Structural Bioinformatics. P. E. Bourne and H. Weissig.Hoboken. NJ. John Wiley & Sons. Inc.: 41-73.

Benoff. B. Yang. H. Lawson. C. Parkinson. G. Liu. J. Blatter. E. Ebright. YW. Berman. HM. Ebright. RH (2002) Structural basis of transcription activation: The CAP-alphaCTD-DNA complex. Science 297:1562-1566.