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Helen Berman

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X Ray Crystallography

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Publications

TOP 3
Helen M Berman; Buvaneswari Coimbatore Narayanan; Luigi Di Costanzo; Shuchismita Dutta; Sutapa Ghosh; Brian P Hudson; Catherine L Lawson; Ezra Peisach; Andreas Prlić; Peter W Rose; Chenghua Shao; Huanwang Yang; Jasmine Young; Christine Zardecki
Trendspotting in the protein data bank.
Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
The future of the protein data bank.
Helen M Berman
Creating a community resource for protein science.

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2013: Helen M Berman; Buvaneswari Coimbatore Narayanan; Luigi Di Costanzo; Shuchismita Dutta; Sutapa Ghosh; Brian P Hudson; Catherine L Lawson; Ezra Peisach; Andreas Prlić; Peter W Rose; Chenghua Shao; Huanwang Yang; Jasmine Young; Christine Zardecki
Trendspotting in the protein data bank.
FEBS letters 2013;587(8):1036-45.
2013: Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
The future of the protein data bank.
Biopolymers 2013;99(3):218-22.
2012: Helen M Berman
Creating a community resource for protein science.
Protein science : a publication of the Protein Society 2012;21(11):1587-96.
2012: Lida K Gifford; Helen M Berman; Lester G Carter; Margaret J Gabanyi; Paul D Adams
The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.
Journal of structural and functional genomics 2012;13(2):57-62.
2012: Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John Lute Markley
The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Structure (London, England : 1993) 2012;20(3):391-6.
2012: Richard Henderson; Wen Jiang; Gerard J Kleywegt; Matthew L Baker; Helen M Berman; Bridget Carragher; Wah Chiu; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Andrej Sali; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Catherine L Lawson
Outcome of the first electron microscopy validation task force meeting.
Structure (London, England : 1993) 2012;20(2):205-14.
2011: Margaret J Gabanyi; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Torsten Schwede; Raship Shah; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Helen M Berman
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.
Journal of structural and functional genomics 2011;12(2):45-54.
2011: Wolfgang F Bluhm; Bojan Beran; Chunxiao Bi; Dimitris Dimitropoulos; Andreas Prlic; Gregory B Quinn; Peter W Rose; Chaitali Shah; Jasmine Young; Benjamin Yukich; Helen M Berman; Philip E Bourne
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Database : the journal of biological databases and curation 2011;2011():bar003.
2009: Shuchismita Dutta; Kyle Burkhardt; Jasmine Young; Ganesh J Swaminathan; Takanori Matsuura; Kim Henrick; Haruki Nakamura; Helen M Berman
Data deposition and annotation at the worldwide protein data bank.
Molecular biotechnology 2009;42(1):1-13.
2008: Catherine L Lawson; Shuchismita Dutta; John D Westbrook; Kim Henrick; Helen M Berman
Representation of viruses in the remediated PDB archive.
Acta crystallographica. Section D, Biological crystallography 2008;D64(Pt 8):874-82.
2008: John Lute Markley; Eldon L Ulrich; Helen M Berman; Kim Henrick; Haruki Nakamura; Hideo Akutsu
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.
Journal of biomolecular NMR 2008;40(3):153-5.
2008: Jane S Richardson; Bohdan Schneider; Laura W Murray; Gary Kapral; Robert M Immormino; Jeffrey J Headd; David C Richardson; Daniela Ham; Eli Hershkovits; Loren Dean Williams; Kevin S Keating; Anna Marie Pyle; David Micallef; John Westbrook; Helen M Berman
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
RNA (New York, N.Y.) 2008;14(3):465-81.
2008: Shuchismita Dutta; Kyle Burkhardt; Ganesh J Swaminathan; Takashi Kosada; Kim Henrick; Haruki Nakamura; Helen M Berman
Data deposition and annotation at the worldwide protein data bank.
Methods in molecular biology (Clifton, N.J.) 2008;426():81-101.
2008: Helen M Berman
Harnessing knowledge from structural genomics.
Structure (London, England : 1993) 2008;16(1):16-8.
2008: Helen M Berman
The Protein Data Bank: a historical perspective.
Acta crystallographica. Section A, Foundations of crystallography 2008;64(Pt 1):88-95.
2008: Kim Henrick; Zukang Feng; Wolfgang F Bluhm; Dimitris Dimitropoulos; Jurgen F Doreleijers; Shuchismita Dutta; Judith L Flippen-Anderson; John Ionides; Chisa Kamada; Evgeny Krissinel; Catherine L Lawson; John Lute Markley; Haruki Nakamura; Richard Newman; Yukiko Shimizu; Jawahar Swaminathan; Sameer Velankar; Jeramia Ory; Eldon L Ulrich; Wim Vranken; John Westbrook; Reiko Yamashita; Huanwang Yang; Jasmine Young; Muhammed Yousufuddin; Helen M Berman
Remediation of the protein data bank archive.
Nucleic acids research 2008;36(Database issue):D426-33.
2007: Helen M Berman; Kim Henrick; Haruki Nakamura; John Lute Markley; Philip Bourne; John Westbrook
Realism about PDB.
Nature biotechnology 2007;25(8):845-6; author reply 846.
2006: Jordi Bella; Jingsong Liu; Rachel Kramer; Barbara Brodsky; Helen M Berman
Conformational effects of Gly-X-Gly interruptions in the collagen triple helix.
Journal of molecular biology 2006;362(2):298-311.
2006: Helen M Berman; Stephen K Burley; Wah Chiu; Andrej Sali; Alexei A Adzhubei; Philip Bourne; Stephen H Bryant; Roland L Dunbrack; Krzysztof Fidelis; Joachim Frank; Adam Godzik; Kim Henrick; Andrzej Joachimiak; Bernard Heymann; David Jones; John Lute Markley; John Moult; Gaetano T Montelione; Christine Orengo; Michael G Rossmann; Burkhard Rost; Helen R Saibil; Torsten Schwede; Daron M Standley; John D Westbrook
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure (London, England : 1993) 2006;14(8):1211-7.
2006: Andrew Napoli; Catherine L Lawson; Richard H. Ebright; Helen M Berman
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
Journal of molecular biology 2006;357(1):173-83.
2006: Andrei Kouranov; Lei Xie; Joanna de la Cruz; Li Chen; John Westbrook; Philip Bourne; Helen M Berman
The RCSB PDB information portal for structural genomics.
Nucleic acids research 2006;34(Database issue):D302-5.
2005: John Westbrook; Nobutoshi Ito; Haruki Nakamura; Kim Henrick; Helen M Berman
PDBML: the representation of archival macromolecular structure data in XML.
Bioinformatics (Oxford, England) 2005;21(7):988-92.
2005: Shuchismita Dutta; Helen M Berman
Large macromolecular complexes in the Protein Data Bank: a status report.
Structure (London, England : 1993) 2005;13(3):381-8.
2005: Helen M Berman; Lynn F Ten Eyck; David S Goodsell; Nina M Haste; Alexandr Kornev; Susan S Taylor
The cAMP binding domain: an ancient signaling module.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(1):45-50.
2005: Nita Deshpande; Kenneth J Addess; Wolfgang F Bluhm; Jeffrey C Merino-Ott; Wayne Townsend-Merino; Qing Zhang; Charlie Knezevich; Lie Xie; Li Chen; Zukang Feng; Rachel Kramer Green; Judith L Flippen-Anderson; John Westbrook; Helen M Berman; Philip Bourne
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.
Nucleic acids research 2005;33(Database issue):D233-7.
2004: Li Chen; Rose Oughtred; Helen M Berman; John Westbrook
TargetDB: a target registration database for structural genomics projects.
Bioinformatics (Oxford, England) 2004;20(16):2860-2.
2004: Huanwang Yang; Vladimir Guranovic; Shuchismita Dutta; Zukang Feng; Helen M Berman; John D Westbrook
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 10):1833-9.
2004: Zukang Feng; Li Chen; Himabindu Maddula; Ozgur Akcan; Rose Oughtred; Helen M Berman; John Westbrook
Ligand Depot: a data warehouse for ligands bound to macromolecules.
Bioinformatics (Oxford, England) 2004;20(13):2153-5.
2004: Catherine L Lawson; Brian Benoff; Tatyana Berger; Helen M Berman; Jannette Carey
E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
Structure (London, England : 1993) 2004;12(6):1099-108.
2004: Philip Bourne; John Westbrook; Helen M Berman
The Protein Data Bank and lessons in data management.
Briefings in bioinformatics 2004;5(1):23-30.
2004: Catherine L Lawson; David Swigon; Katsuhiko S Murakami; Seth A Darst; Helen M Berman; Richard H. Ebright
Catabolite activator protein: DNA binding and transcription activation.
Current opinion in structural biology 2004;14(1):10-20.
2004: William A McLaughlin; Daniel W Kulp; Joanna de la Cruz; Xiang-Jun Lu; Catherine L Lawson; Helen M Berman
A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
Journal of structural and functional genomics 2004;5(4):255-65.
2004: Helen M Berman; John D Westbrook
The impact of structural genomics on the protein data bank.
American journal of pharmacogenomics : genomics-related research in drug development and clinical practice 2004;4(4):247-52.
2004: Philip Bourne; Kenneth J Addess; Wolfgang F Bluhm; Li Chen; Nita Deshpande; Zukang Feng; Ward Fleri; Rachel Green; Jeffrey C Merino-Ott; Wayne Townsend-Merino; Helge Weissig; John Westbrook; Helen M Berman
The distribution and query systems of the RCSB Protein Data Bank.
Nucleic acids research 2004;32(Database issue):D223-5.
2003: William A McLaughlin; Helen M Berman
Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif.
Journal of molecular biology 2003;330(1):43-55.
2003: John Westbrook; Zukang Feng; Kyle Burkhardt; Helen M Berman
Validation of protein structures for protein data bank.
Methods in enzymology 2003;374():370-85.
2003: Helen M Berman; John Westbrook
The need for dictionaries, ontologies, and controlled vocabularies.
Omics : a journal of integrative biology 2003;7(1):9-10.
2003: Helen M Berman; John Westbrook; Zukang Feng; Lisa Iype; Bodhan Schneider; Christine Zardecki
The nucleic acid database.
Methods of biochemical analysis 2003;44():199-216.
2003: John Westbrook; Zukang Feng; Li Chen; Huanwang Yang; Helen M Berman
The Protein Data Bank and structural genomics.
Nucleic acids research 2003;31(1):489-91.
2002: Brian Benoff; Huanwang Yang; Catherine L Lawson; Gary Parkinson; Jinsong Liu; Erich Blatter; Yon W Ebright; Helen M Berman; Richard H. Ebright
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.
Science (New York, N.Y.) 2002;297(5586):1562-6.
2002: Helen M Berman; Tammy Battistuz; Talapady N Bhat; Wolfgang F Bluhm; Philip Bourne; Kyle Burkhardt; Zukang Feng; Gary L Gilliland; Lisa Iype; Shri Jain; Phoebe Fagan; Jessica Marvin; David Padilla; Veerasamy Ravichandran; Bohdan Schneider; Narmada Thanki; Helge Weissig; John D Westbrook; Christine Zardecki
The Protein Data Bank.
Acta crystallographica. Section D, Biological crystallography 2002;58(Pt 6 No 1):899-907.
2002: Helen M Berman; John Westbrook; Zukang Feng; Lisa Iype; Bohdan Schneider; Christine Zardecki
The Nucleic Acid Database.
Acta crystallographica. Section D, Biological crystallography 2002;58(Pt 6 No 1):889-98.
2002: John Westbrook; Zukang Feng; Shri Jain; Talapady N Bhat; Narmada Thanki; Veerasamy Ravichandran; Gary L Gilliland; Wolfgang F Bluhm; Helge Weissig; Douglas S Greer; Philip Bourne; Helen M Berman
The Protein Data Bank: unifying the archive.
Nucleic acids research 2002;30(1):245-8.
2001: S Chen; A Gunasekera; X Zhang; T A Kunkel; Richard H. Ebright; Helen M Berman
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking.
Journal of molecular biology 2001;314(1):75-82.
2001: S Chen; J Vojtechovsky; G N Parkinson; Richard H. Ebright; Helen M Berman
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.
Journal of molecular biology 2001;314(1):63-74.
2001: Wilma K Olson; M Bansal; S K Burley; R E Dickerson; M Gerstein; Stephen C Harvey; U Heinemann; Xiang-Jun Lu; S Neidle; Zippora Shakked; Heinz Sklenar; M Suzuki; C S Tung; E Westhof; Cynthia Wolberger; Helen M Berman
A standard reference frame for the description of nucleic acid base-pair geometry.
Journal of molecular biology 2001;313(1):229-37.
2001: RZ Kramer; Jordi Bella; Barbara Brodsky; Helen M Berman
The crystal and molecular structure of a collagen-like peptide with a biologically relevant sequence.
Journal of molecular biology 2001;311(1):131-47.
2001: Talapady N Bhat; P Bourne; Zukang Feng; Gary L Gilliland; Shri Jain; Veerasamy Ravichandran; B Schneider; K Schneider; Narmada Thanki; Helge Weissig; John Westbrook; Helen M Berman
The PDB data uniformity project.
Nucleic acids research 2001;29(1):214-8.
2000: Helen M Berman; Talapady N Bhat; Philip Bourne; Zukang Feng; Gary L Gilliland; Helge Weissig; John Westbrook
The Protein Data Bank and the challenge of structural genomics.
Nature structural biology 2000;7 Suppl():957-9.
2000: RZ Kramer; M G Venugopal; Jordi Bella; P Mayville; Barbara Brodsky; Helen M Berman
Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair.
Journal of molecular biology 2000;301(5):1191-205.
2000: Jordi Bella; Helen M Berman
Integrin-collagen complex: a metal-glutamate handshake.
Structure (London, England : 1993) 2000;8(6):R121-6.
2000: Helen M Berman; John Westbrook; Zukang Feng; Gary L Gilliland; Talapady N Bhat; Helge Weissig; Ilya N Shindyalov; Philip Bourne
The Protein Data Bank.
Nucleic acids research 2000;28(1):235-42.
1999: RZ Kramer; Jordi Bella; P Mayville; Barbara Brodsky; Helen M Berman
Sequence dependent conformational variations of collagen triple-helical structure.
Nature structural biology 1999;6(5):454-7.
1998: S C Jain; Ujwal Shinde; Y Li; M Inouye; Helen M Berman
The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution.
Journal of molecular biology 1998;284(1):137-44.
1998: Helen M Berman; Christine Zardecki; John Westbrook
The Nucleic Acid Database: A resource for nucleic acid science.
Acta crystallographica. Section D, Biological crystallography 1998;54(Pt 6 Pt 1):1095-104.
1998: J Woda; B Schneider; K Patel; K Mistry; Helen M Berman
An analysis of the relationship between hydration and protein-DNA interactions.
Biophysical journal 1998;75(5):2170-7.
1998: RZ Kramer; Helen M Berman
Patterns of hydration in crystalline collagen peptides.
Journal of biomolecular structure & dynamics 1998;16(2):367-80.
1998: RZ Kramer; Luigi Vitagliano; Jordi Bella; Rita Berisio; Lelio Mazzarella; Barbara Brodsky; Adriana Zagari; Helen M Berman
X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly).
Journal of molecular biology 1998;280(4):623-38.
1997: Helen M Berman
Crystal studies of B-DNA: the answers and the questions.
Biopolymers 1997;44(1):23-44.
1996: Jordi Bella; Helen M Berman
Crystallographic evidence for C alpha-H...O=C hydrogen bonds in a collagen triple helix.
Journal of molecular biology 1996;264(4):734-42.
1996: G Parkinson; C Wilson; A Gunasekera; Y W Ebright; R E Ebright; Richard H. Ebright; Helen M Berman
Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface.
Journal of molecular biology 1996;260(3):395-408.
1996: G Parkinson; J Vojtechovsky; L Clowney; A T Brünger; Helen M Berman
New parameters for the refinement of nucleic acid-containing structures.
Acta crystallographica. Section D, Biological crystallography 1996;52(Pt 1):57-64.
1996: Helen M Berman; A Gelbin; J Westbrook
Nucleic acid crystallography: a view from the nucleic acid database.
Progress in biophysics and molecular biology 1996;66(3):255-88.
1996: Jordi Bella; Barbara Brodsky; Helen M Berman
Disrupted collagen architecture in the crystal structure of a triple-helical peptide with a Gly-->Ala substitution.
Connective tissue research 1996;35(1-4):401-6.
1995: J Vojtechovsky; M D Eaton; B Gaffney; R Jones; Helen M Berman
Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs.
Biochemistry 1995;34(51):16632-40.
1995: G N Parkinson; G M Arvanitis; L Lessinger; S L Ginell; R Jones; B Gaffney; Helen M Berman
Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative.
Biochemistry 1995;34(47):15487-95.
1995: Jordi Bella; Barbara Brodsky; Helen M Berman
Hydration structure of a collagen peptide.
Structure (London, England : 1993) 1995;3(9):893-906.
1995: Matthew Adam Young; G Ravishanker; David L Beveridge; Helen M Berman
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
Biophysical journal 1995;68(6):2454-68.
1994: Jordi Bella; M Eaton; Barbara Brodsky; Helen M Berman
Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution.
Science (New York, N.Y.) 1994;266(5182):75-81.
1994: S L Ginell; J Vojtechovsky; B Gaffney; R Jones; Helen M Berman
Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine.
Biochemistry 1994;33(12):3487-93.
1994: G N Parkinson; Y Wu; P Fan; Joachim Kohn; J Baum; Helen M Berman
Crystal structure and NMR conformation of a cyclic pseudotetrapeptide containing urethane backbone linkages.
Biopolymers 1994;34(3):403-14.
1993: B Schneider; D M Cohen; L Schleifer; A R Srinivasan; Wilma K Olson; Helen M Berman
A systematic method for studying the spatial distribution of water molecules around nucleic acid bases.
Biophysical journal 1993;65(6):2291-303.
1993: Nancy Pleshko Camacho; D R Smith; A Goldman; B Schneider; D Green; Peter Young; Helen M Berman
Structure of an interleukin-1 beta mutant with reduced bioactivity shows multiple subtle changes in conformation that affect protein-protein recognition.
Biochemistry 1993;32(34):8749-57.
1992: B Schneider; S L Ginell; Helen M Berman
Low temperature structures of dCpG-proflavine. Conformational and hydration effects.
Biophysical journal 1992;63(6):1572-8.
1992: B Schneider; S L Ginell; R Jones; B Gaffney; Helen M Berman
Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers.
Biochemistry 1992;31(40):9622-8.
1992: Helen M Berman; Joel Sussman; Leemor Joshua-Tor; G G Revich; L S Ripley
A structural model for sequence-specific proflavin-DNA interactions during in vitro frameshift mutagenesis.
Journal of biomolecular structure & dynamics 1992;10(2):317-31.
1992: Helen M Berman; Wilma K Olson; David L Beveridge; J Westbrook; A Gelbin; T Demeny; S H Hsieh; A R Srinivasan; B Schneider
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.
Biophysical journal 1992;63(3):751-9.
1992: B Schneider; D Cohen; Helen M Berman
Hydration of DNA bases: analysis of crystallographic data.
Biopolymers 1992;32(7):725-50.
1991: N Narayana; S L Ginell; I M Russu; Helen M Berman
Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG).
Biochemistry 1991;30(18):4449-55.
1990: S L Ginell; S Kuzmich; R A Jones; Helen M Berman
Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine.
Biochemistry 1990;29(46):10461-5.
1990: P S Subramanian; S Pitchumani; David L Beveridge; Helen M Berman
A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: comparison with crystallographic ordered water sites.
Biopolymers 1990;29(4-5):771-83.
1988: S Ginell; L Lessinger; Helen M Berman
The crystal and molecular structure of the anticancer drug actinomycin D--some explanations for its unusual properties.
Biopolymers 1988;27(5):843-64.
1988: Helen M Berman; A Sowri; S Ginell; David L Beveridge
A systematic study of patterns of hydration in nucleic acids:(I) guanine and cytosine.
Journal of biomolecular structure & dynamics 1988;5(5):1101-10.
1983: Mihaly Mezei; David L Beveridge; Helen M Berman; J M Goodfellow; J L Finney; S Neidle
Monte Carlo studies on water in the dCpG/proflavin crystal hydrate.
Journal of biomolecular structure & dynamics 1983;1(1):287-97.