Research Topics
| H M BermanSummaryAffiliation: Rutgers University Country: USA Publications
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Detail Information
Publications
The Protein Data Bank at 40: reflecting on the past to prepare for the futureHelen M Berman
RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Structure 20:391-6. 2012..PDB40's distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field...- The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methodsMargaret J Gabanyi
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
J Struct Funct Genomics 12:45-54. 2011.... - The Protein Data Bank: a historical perspectiveHelen M Berman
Rutgers, The State University of New Jersey, USA
Acta Crystallogr A 64:88-95. 2008..The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource... - The impact of structural genomics on the protein data bankHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
Am J Pharmacogenomics 4:247-52. 2004..The PDB has developed tools to facilitate the rapid deposition of data produced by the structural genomics initiatives and has created databases to track the progress of the work... - The need for dictionaries, ontologies, and controlled vocabulariesHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
OMICS 7:9-10. 2003 - The cAMP binding domain: an ancient signaling moduleHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
Proc Natl Acad Sci U S A 102:45-50. 2005..The modified positioning of the helix in turn is recognized by a protein-binding event, completing the allostery... - Outcome of a workshop on archiving structural models of biological macromoleculesHelen M Berman
The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
Structure 14:1211-7. 2006 - The Protein Data BankHelen M Berman
RCSB, Department of Chemistry, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, USA
Acta Crystallogr D Biol Crystallogr 58:899-907. 2002..The reader should come away with an understanding of the scope of the PDB and what is provided by the resource... - The Nucleic Acid DatabaseHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
Acta Crystallogr D Biol Crystallogr 58:889-98. 2002..The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article... - The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB dataHelen Berman
RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
Nucleic Acids Res 35:D301-3. 2007..The wwPDB website at http://www.wwpdb.org/ provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB... - The past and future of structure databasesH M Berman
Department of Chemistry Rutgers University 610 Taylor Road Piscataway NJ 08854 8087 USA
Curr Opin Biotechnol 10:76-80. 1999..Currently available are databases that classify molecules according to their overall structural characteristics or particular features of structures, as well as databases that focus on particular protein families in depth... - The protein structure initiative structural genomics knowledgebaseHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Nucleic Acids Res 37:D365-8. 2009..By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities... - The Protein Data BankH M Berman
Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
Nucleic Acids Res 28:235-42. 2000..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource... - The Protein Data Bank and the challenge of structural genomicsH M Berman
Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway 08854 8087, USA
Nat Struct Biol 7:957-9. 2000..The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics... - Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data BankHuanwang Yang
Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Acta Crystallogr D Biol Crystallogr 60:1833-9. 2004..The options, procedures and tools for accurate and automated PDB data deposition are described here... - Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motifWilliam A McLaughlin
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway 08854 8087, USA
J Mol Biol 330:43-55. 2003.... - Structural basis of transcription activation: the CAP-alpha CTD-DNA complexBrian Benoff
Waksman Institute and Department of Chemistry, Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA
Science 297:1562-6. 2002..These findings are consistent with the proposal that activation involves a simple "recruitment" mechanism... - The Protein Data Bank: unifying the archiveJohn Westbrook
Rutgers, The State University of New Jersey, Department of Chemistry, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Nucleic Acids Res 30:245-8. 2002..rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software... - The RCSB PDB information portal for structural genomicsAndrei Kouranov
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Nucleic Acids Res 34:D302-5. 2006..Functional coverage can be examined according to enzyme classification, gene ontology (biological process, cell component and molecular function) and disease... - Ligand Depot: a data warehouse for ligands bound to macromoleculesZukang Feng
Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
Bioinformatics 20:2153-5. 2004..rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux... - TargetDB: a target registration database for structural genomics projectsLi Chen
Research Collaboratory for Structural Bioinformatics, Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
Bioinformatics 20:2860-2. 2004..AVAILABILITY: TargetDB is available at http://targetdb.pdb.org/.. - Catabolite activator protein: DNA binding and transcription activationCatherine L Lawson
Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA
Curr Opin Struct Biol 14:10-20. 2004.... - Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine stepsAndrew A Napoli
Department of Chemistry and Chemical Biology and Waksman Institute Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
J Mol Biol 357:173-83. 2006.... - Harnessing knowledge from structural genomicsHelen M Berman
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Structure 16:16-8. 2008 - Data deposition and annotation at the worldwide protein data bankShuchismita Dutta
Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Methods Mol Biol 426:81-101. 2008..This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included... - Representation of viruses in the remediated PDB archiveCatherine L Lawson
RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
Acta Crystallogr D Biol Crystallogr . 2008..Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive... - Data deposition and annotation at the worldwide protein data bankShuchismita Dutta
Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 8087, USA
Mol Biotechnol 42:1-13. 2009..This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included... - PDBML: the representation of archival macromolecular structure data in XMLJohn Westbrook
Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey 610 Taylor Road, Piscataway, NJ 08854, USA
Bioinformatics 21:988-92. 2005..The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files... - Signatures of protein-DNA recognition in free DNA binding sitesJason W Locasale
Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
J Mol Biol 386:1054-65. 2009..Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition... - E. coli trp repressor forms a domain-swapped array in aqueous alcoholCatherine L Lawson
Rutgers University, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854, USA
Structure 12:1099-108. 2004..Small angle X-ray scattering measurements show that the self-association properties of trpR in solution are fundamentally altered by isopropanol... - EMDataBank.org: unified data resource for CryoEMCatherine L Lawson
Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
Nucleic Acids Res 39:D456-64. 2011.... - The Nucleic Acid Database: A resource for nucleic acid scienceH M Berman
NDB, Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
Acta Crystallogr D Biol Crystallogr 54:1095-104. 1998..Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given... - Three-dimensional EM structure of an intact activator-dependent transcription initiation complexBrian P Hudson
Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA
Proc Natl Acad Sci U S A 106:19830-5. 2009..The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits... - A structure-based method for identifying DNA-binding proteins and their sites of DNA-interactionWilliam A McLaughlin
Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
J Struct Funct Genomics 5:255-65. 2004..For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA... - Validation of protein structures for protein data bankJohn Westbrook
Department of Chemistry, Rutgers State University of New York, Piscataway, New Jersey 08854, USA
Methods Enzymol 374:370-85. 2003 - The Protein Data Bank and structural genomicsJohn Westbrook
Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Nucleic Acids Res 31:489-91. 2003.... - Large macromolecular complexes in the Protein Data Bank: a status reportShuchismita Dutta
The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
Structure 13:381-8. 2005..Some of the challenges at the PDB in representing, archiving, visualizing, and analyzing these structures are discussed along with possible means to overcome them... - The nucleic acid databaseHelen M Berman
Department of Chemistry, Rutgers University, Piscataway, NJ, USA
Methods Biochem Anal 44:199-216. 2003 - Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinkingS Chen
Department of Chemistry and The Waksman Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
J Mol Biol 314:63-74. 2001..We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence... - Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interfaceG Parkinson
Department of Chemistry and The Waksman Institute, Rutgers University, New Brunswick, NJ 08855 0939, USA
J Mol Biol 260:395-408. 1996..In addition, the present resolution permits accurate definition of the kinked DNA conformation in the CAP-DNA complex... - Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinkingS Chen
Department of Chemistry and The Waksman Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854 8087, USA
J Mol Biol 314:75-82. 2001..The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7)... - Conformational effects of Gly-X-Gly interruptions in the collagen triple helixJordi Bella
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
J Mol Biol 362:298-311. 2006..The structure suggests a role for Gly-X-Gly interruptions as defining regions of flexibility and molecular recognition in the otherwise relatively uniform repeating collagen conformation... - The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolutionS C Jain
Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ, 08854 8087, USA
J Mol Biol 284:137-44. 1998..The structure determination reported here provides additional information about the nature of the interaction between the subtilisin and propeptide domains in this complex... - The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schemaNita Deshpande
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Nucleic Acids Res 33:D233-7. 2005..The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described... - Remediation of the protein data bank archiveKim Henrick
MSD EBI, EMBL Outstation Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 36:D426-33. 2008..The scope and methods used in this project are presented... - Realism about PDBHelen M Berman
Nat Biotechnol 25:845-6; author reply 846. 2007 - The Protein Data Bank and lessons in data managementPhilip E Bourne
Department of Pharmacology and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0537, USA
Brief Bioinform 5:23-30. 2004..The role of the human factor in the form of users, collaborators, scientific society and ad hoc committees is also included... - The distribution and query systems of the RCSB Protein Data BankPhilip E Bourne
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
Nucleic Acids Res 32:D223-5. 2004..The PDB's mandate is to disseminate this information in the most usable form and as widely as possible. The current query and distribution system is described and an alpha version of the future re-engineered system introduced... - Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteinsSusan Jones
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 31:7189-98. 2003..This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set... - RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)Jane S Richardson
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710 3711, USA
RNA 14:465-81. 2008..The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs... - Fundamentals of DNA and RNA structureStephen Neidle
Structural Biology Section, CRC Biomolecular Structure Unit, Institute of Cancer Research, London, UK
Methods Biochem Anal 44:41-73. 2003 - BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositionsJohn L Markley
Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
J Biomol NMR 40:153-5. 2008..The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems... - The RNA Ontology Consortium: an open invitation to the RNA communityNeocles B Leontis
RNA 12:533-41. 2006....
Research Grants
- BIOMOLECULAR STRUCTURE AND INTERACTIONSHelen Berman; Fiscal Year: 1999..We plan to determine the structures of a series of model collagen peptides with the goal of understanding how collagen assembles and interacts with other molecules in its environment. ..
- NUCLEIC ACID STRUCTURES AND INTERACTIONSHelen Berman; Fiscal Year: 1993..We will also continue pilot studies on the nucleotide binding enzyme, AMP nucleosidase with the goal of producing crystals suitable for a full x-ray crystallographic analysis...
- BIOMOLECULAR STRUCTURE AND INTERACTIONSHelen Berman; Fiscal Year: 2002..In addition, we are determining the structures of selected oligonucleotides in an attempt to understand the effects of sequence and environment on DNA structure. ..