Helen M. Berman



Total Publications (252)


1.    "Anomeric Bond-Character in the Pyranose Sugars", H. M. Berman, S. S. C. Chu, and G. A. Jeffrey,Science, 157:1576-1577, 1967.

2.    "A Second Determination of the Structure of Hydroxyurea", H. M. Berman and S. H. Kim, Acta Cryst.,23:180-181, 1967.

3.   "The Crystal Structure of Galactitol", H. M. Berman and R. D. Rosenstein, Acta Cryst., B24:435-441, 1968.

4.   "The Crystal Structure of the a' and b Forms of D-Mannitol", H. M. Berman, G. A. Jeffrey, and R. D. Rosenstein, Acta Cryst., B24:442-449, 1968.

5.   "The Crystal Structure of Methyl a-D-Glucopyranoside", H. M. Berman and S. H. Kim, Acta Cryst., B24:897-904, 1968.

6.   "The Crystal Structure of L-Azetidine-2-Carboxylic Acid. A Naturally occurring Homolog of Proline", H. M. Berman, E. L. McGandy, R. Van Etten, and J. Burgner, Am. Chem. Soc., 91:6177-6182, 1969.

7.   "The Crystal Structure of N-Methyl-N-t-butyl-3-hydroxyazetidinium Methanesulfonate, a Nonplanar Azetidinium Ring", E. L. McGandy, H. M. Berman, R. Van Etten, and J. Burgner, J. Am. Chem. Soc.,91:6173-6177, 1969.

8.   "The Crystal Structure of a Trisaccharide, Raffinose Pentahydrate", H. M. Berman, Acta Cryst., B26:290-299, 1970.

9.   "The Crystal Structure of g-D-Gulonolactone", H. M. Berman, R. D. Rosenstein, and J. Southwick, Acta Cryst.,B27:7-10, 1971.

10.   "Nucleic Acid Conformation:  Crystal Structure of a Naturally Occurring Dinucleoside Phosphate UpA", N. C. Seeman, J. L. Sussman, H. M. Berman, and S. H. Kim, Nat. New Biol., 233:90-92, 1971.

11.   "The Crystal Structure of D-iso-Ascorbic Acid", N. Azarnia, H. M. Berman, and R. D. Rosenstein, Acta Cryst., B28:2157-2161, 1972.

12.   "The Crystal Structure of ICR-170-OH, An Analogue of an Antitumor Agent and Mutagen", H. M. Berman and J. P. Glusker, Acta Cryst., B28:590-596, 1972.

13.   "The Crystal Structure of Potassium Dihydrogen trans-Aconitate", J. M. Dargay, H. M. Berman, J. P. Glusker, and H. L. Carrell, Acta Cryst., B28:1533-1539, 1972.

14.   "The Crystal Structure of a Naturally Occurring Dinucleoside Phosphate Uridylyl 3'5' Adenosine Phosphate", J. L. Sussman, N. C. Seeman, S. H. Kim, and H. M. Berman, J. Mol. Biol., 66:403-421, 1972.

15.   "The Crystal Structure of 10-Chloromethyl-2,3,9-trimethylanthracene", A. Chomyn, J. P. Glusker, H. M. Berman, and H. L. Carrell, Acta Cryst.,B28:3512-3517, 1972.

16.   "Seven Basic Conformations of Nucleic Acid Structural Units", S. H. Kim, H. M. Berman, M. D. Newton, and N. C. Seeman, Acta Cryst., B29:703-710, 1973.

17.   "Crystal Structure of an Anti Viral Agent: 5-[N-(L-Phenylalanyl)amino]uridine", H. M. Berman, W. C. Hamilton, and R. Rousseau, Biochemistry,9:1809-1814, 1973.

18.   "Synthesis of 4-amino-8-(b-D-ribofuranosyl) Amino Pyrimido [5,4-d] Pyrimidine from a Purine Nucleoside - A Novel Rearrangement of the Purine Ring", H. M. Berman, R. J. Rousseau, R. W. Mancuso, G. P. Kreishman, and R. K. Robins, Tetrahedron Lett., 33:3099-3101, 1973.

19.   "Refinement of the Structure of Potassium Hydrogen Isocitrate Lactone", H. M. Berman, H. L. Carrell, and J. P. Glusker, Acta Cryst., B29:1163-1165, 1973.

20.   "X-ray Crystallography of Biological Molecules", H. M. Berman in Spectroscopy in Biology and Chemistry, S-H. Chen and S. Yip, Eds., Academic Press Inc., pp. 145-175, 1974.

21.   "Crystallographic Studies of D-Xylose Isomerase", H. M. Berman, B. H. Rubin, H. L. Carrell, and J. P. Glusker, J. Biol. Chem., 249:3983-3984, 1974.

22.   "CRYSNET, a crystallographic computing network with interactive graphics display", E. F. Meyer, Jr., C. N. Morimoto, J. Villarreal, H. M. Berman, H. L. Carrell, R. K. Stodola, T. F. Koetzle, L. D. Andrews, F. C. Bernstein, and H. J. Bernstein, Proceedings from the FASEB Conference on the Computer as a Research Tool in the Life Sciences, 33:2402-2405, 1974.

23.   "Crystal and Molecular Structure of a Caged Polycyclic Tetraoxycarbophosphorane", H. L. Carrell, H. M. Berman, J. S. Ricci, Jr., W. C. Hamilton, F. Ramirez, J. F. Maracek, L. Kramer, and I. Ugi, J. Am. Chem. Soc., 97:38-46, 1975.

24.   "The Crystal Structure of a Uracil-Acetone Photoaddition Product", M. T. Stein, H. M. Berman, and A. J. Varghese, Biochim. Biophys. Acta, 407:377-383,1975.

25.   "A Crystallographic Determination of a Chemical Structure:  6-amino-10-(b-D-ribofuranosylamino)pyrimido-[5,4-d]pyrimidine, An Example of An Unusual D-Ribose Conformation",  P. Narayanan and H. M. Berman,Carbohydr. Res., 44:169-180, 1975.

26.   "2-[3-(7-Chloro-2-methoxy-10-[benzo[b]-1,5-naphthyridinyl]amino)propyl-amino] ethanol (ICR-372-OH)", J. P. Glusker, H. L. Carrell, H. M. Berman, and B. Gallen, Acta Cryst., B31:826-831, 1975.

27.   "A Restitution" (Book Reviews: Rosalind Franklin and DNA by Sayre, Anne), H.M. Berman, Science, Volume 190, Issue 4215, pp. 665, 1975.

28.   "a-S Cysteinylthymine: A Model for Protein-Nucleic Acid Cross-Linking", H. M. Berman, D. E. Zacharias, H. L. Carrell, and A. J. Varghese, Biochemistry, 15:463-467, 1976.

29.   "Aggregation of Acridine Orange:  Crystal Structure of Acridine Orange Tetrachlorozincate 2C17H19N3•2HCl•ZnCl2•CH3COOH", S. K. Obendorf, J. P. Glusker, P .R. Hansen, H. M. Berman, and H. L. Carrell, Bioinorg. Chem., 6:29-44,1976.

30.   "Model Compounds for Protein Nucleic Acid Interactions. 3. Synthesis and Structure of a Nucleoside Dipeptide, N-(9-b-D-Ribofuranosylpurin-6-yl)glycyl-L-alanine Sesquihydrate",  P. Narayanan, H. M. Berman and R. Rousseau, J. Am. Chem. Soc., 98:8472-8475,1976.

31.   "Characterization of a Monoclinic Crystal Form of an Enzyme of Steroid Metabolism    5-3-Ketosteroid Isomerase", E. M. Westbrook, P. J. Sigler, H. M. Berman, J. P. Glusker, G. Bunick, A. Benson, and P. Talalay, J. Mol. Biol.,103:665-667, 1976.

32.   "Model Compounds for Protein Nucleic Acid Interactions.  IV.  Crystal Structure of a Nucleoside Peptide with Anti-Viral Properties:  5-[N-(L-Leucyl)amino]uridine", P. Narayanan and H. M. Berman,Acta Cryst., B33:2047-2051, 1977.

33.   "Model Compounds for Protein-Nucleic Acid Interactions.  5.1a  5-S-Cysteinyluracil Monohydrate, a Photoaddition Product between an Amino Acid and Pyrimidine Base", G. Williams, A. J. Varghese, and H. M. Berman, J. Am. Chem. Soc., 99:3150-3154, 1977.

34.   "Alkylation of a Tripeptide by a Carcinogen: The Crystal Structures of Sarcosylglycylglycine, 9 Methyl-10-chloromethylanthracene and Their Reaction Product", J. P. Glusker, H. L. Carrell, H. M. Berman, B. Gallen, and R. M. Peck, J. Am. Chem. Soc., 99:595-601, 1977.

35.   "RNA Structure", N. Kallenbach and H. M. Berman, Quar. Rev. of Biophys., 10:138-236, 1977.

36.   "Structure of a dinucleoside phosphate-drug complex as a model for nucleic acid-drug interaction", S. Neidle, A. Achari, G. L. Taylor, H. M. Berman, H. L. Carrell, J. P. Glusker and W. Stallings. Nature, 269:304-307, 1977.

37.   "Crystal Structure of Tetrahymanol Hemihydrate", D. A. Langs, W. L. Duax, H. L. Carrell, H. M. Berman, and E. Caspi, J. Org. Chem., 42:2134-2137, 1977.

38.   "Crystal and Molecular Structure of Oxyphosphoranes. 9.1 The Spiropentaoxyphosphorane, (PO5)(CF3C=CCF3)(C6H4)(C6H5)",  P. Narayanan, H. M. Berman, F. Ramirez, J. F. Marecek, YuFen Chaw, and V. A. V. Prasad, J. Am. Chem. Soc., 99:3336-3342, 1977.

39.   "Drug-nucleic acid interactions: Conformational flexibility at the intercalation site", H. M. Berman, S. Neidle, and R. Stodola, Proc. Natl. Acad. Sci., 75:828-832, 1978.

40.   "Modified bases in tRNA:  the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine", H. M. Berman, D. Marcu, P. Narayanan, J. D. Fissekis, and R. Lipnick, Nucl. Acids Res., 5:893-904, 1978.

41.    "A 1:2 Crystalline Complex of ApA: Proflavine: A Model for Binding to Single Stranded Regions in RNA",  S. Neidle, G. Taylor, M. Sanderson, H. S. Shieh, and H. M. Berman, Nucl. Acids Res.,522, 1978.

42.    "Netropsin, a DNA-Binding Oligopeptide Structural and Binding Studies", H. M. Berman, S. Neidle, C. Zimmer, and H. Thurm, Biochim. Biophys. Acta, 561:124-131,1979.

43.    "Modelling of Drug-Nucleic Acid Interactions Intercalation Geometry of Oligonucleotides", H. M. Berman and S. Neidle in Stereodynamics of Molecular Systems, R. Sarma, Editor, Pergamon, pp. 367-382, 1979.

44.    "Molecular and Crystal Structure of an Intercalation Complex: Proflavine- Cytidylyl-(3'5')-Guanosine", H. M. Berman, W. Stallings, H. L. Carrell, J. P. Glusker, S. Neidle, G. Taylor, and A. Achari, Biopolymers,18:2405-2429, 1979.

45.    "The structure of a drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA Fragments", H. S. Shieh, H. M. Berman, M. Dabrow, and S. Neidle, Nucl. Acids Res., 8:85-97, 1980.

46.    "Highly structured water network in crystals of a deoxydinucleoside-drug complex", S. Neidle, H. M. Berman, and H.S. Shieh, Nature, 288:129-133, 1980.

47.    "The Interaction of Intercalating Drugs with Nucleic Acids", H. M. Berman and P. Young, Ann. Rev. Biophys. Bioeng,10:87-114, 1981.

48.    "Conformational principles of nucleic acids", H. M. Berman in Topics in Nucleic Acid Structure, S. Neidle, Editor, MacMillan Publishing Co., London, pp. 1-17, 1981.

49.    "Crystal Structures of Fragments of DNA and RNA", H. M. Berman and H. S. Shieh in Topics in Nucleic Acid Structure, S. Neidle, Editor, MacMillan Publishing Co., London, pp. 17-33, 1981.

50.   "Determination of the Anomeric Configuration of 2'-Deoxy-D-ribonucleo- sides by 1H NMR and by Crystallographic Studies of a Novel 2'-Deoxy-Nucleoside", P. C. Srivastava, R. K. Robins, F. Takusagawa, and H. M. Berman, J. Heterocycl. Chem.,18:1659-1662, 1981.

51.     "The structure of a pseudo intercalated complex between actinomycin and the DNA binding sequence d(GpC) ", F. Takusagawa, M. Dabrow, S. Neidle, and H. M. Berman,Nature 296:466-469, 1982.

52.     "The Structure of S-Adenosyl-L-homocysteine 2•5-Hydrate", H. S. Shieh and H. M. Berman, Acta Cryst., B38:1513-1517, 1982.

53.     "The Structure of S-8-Azaadenosyl-L-homocysteine (8-aza-SAH): A Synthetic Methyltransferase Inhibitor", V. B. Pett, H. S. Shieh, and H. M. Berman, Acta Cryst., B38:2611-2615, 1982.

54.     "The Structure of a Hydrated 1:2 Complex of Adenylyl(3'5')adenosine-Proflavine Hemisulphate", H‑S. Shieh, H. M. Berman, S. Neidle, G. Taylor, and M. Sanderson, Acta Cryst.,B38:523-531, 1982.

55.     "Drug Intercalation in Nucleic Acids: The Current State of Knowledge", S. Neidle and H. M. Berman, in Molecular Structure and Biological Activity,J. F. Griffin and W. L. Duax, eds., Elsevier Science Publishing Co. Inc., pp. 287-302, 1982.

56.     "The Structure of the Ribodinucleoside Monophosphate Guanylyl-3',5'-cytidine as its Ammonium Octahydrate Salt", A. Aggarwal, S. A. Islam, R. Kuroda, M. R. Sanderson, S. Neidle, and H. M. Berman, Acta Cryst., B39:98-104, 1983.

57.     "X-ray Crystallographic Studies of Nucleic Acids and Nucleic Acid - Drug Complexes", S. Neidle and H. M. Berman, Prog. Biophys. Molec. Biol., 41:43-66, 1983.

58.     "Some New Aspects of Actinomycin D-Nucleic Acid Binding", F. Takusagawa and H. Berman, Cold Spring Harbor Symposia on Quantitative Biology, XLVII: 315-321, 1983.

59.     "Monte Carlo Studies on Water in the dCpG/Proflavin Crystal Hydrate", M. Mezei, D. L. Beveridge, H. M. Berman, J. M. Goodfellow, J. L. Finney, and S. Neidle, J. Biomol. Struc. and Dyn., 1:287-297, 1983.

60.     "Structural Studies of a New Antitumor Agent:  Tiazofurin and its Inactive Analogues",  B. M. Goldstein, F. Takusagawa, H. M. Berman, P. C. Srivastava, and R. K. Robins, J. Am. Chem. Soc., 105:7416-7422, 1983.

61.     "Crystallization and Preliminary X-ray Study of a Complex between d(ATGCAT) and Actinomycin D",  F. Takusagawa, B. M. Goldstein, S. Youngster, R. A. Jones, and H. M. Berman, J. Biol. Chem., 259:4714-4715, 1984.

62.     "Structural Studies of a New Antitumor and Antiviral Agent:  Selenazofurin and Its a-Anomer", B. Goldstein, F. Takusagawa, H. M. Berman, P. Srivastava, and R. Robins, J. Am. Chem. Soc., 107:1394-1400, 1985.

63.     "Structure of N-[1¢-(9-Adenyl)-b-D-ribofuranuronosyl]-L-phenylalanine, Water Ethanol (1/ 1/2/ 1/4), C19H20N6O6×1/2H20×1/4C2H6O", F. Takusagawa, H. M. Berman, M. Dabrow and, R. Robins, Acta Cryst., C41:400-404, 1985.

64.     "Crystalline Hydrates of a Drug-Nucleic Acid Complex", H. M. Berman and S. L. Ginell, in Biomolecular Stereodynamics III, Proceedings of the Fourth Conversation in the Discipline Biomolecular Stereodynamics, State University of New York, Albany, NY, June 4-9, 1985, (Ramaswamy H. Sarma & Mukti H. Sarma, eds.), Adenine Press, 1986.

65.     "Crystal and Molecular Structure of a Chiral-Specific DNA-Binding Agent: Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) ", B. M. Goldstein, J. K. Barton, and H. M. Berman, Inorg. Chem.,25:842-847, 1986.

66.     "Hydration of Nucleic Acid Crystals", H. M. Berman, in Computer Simulation of Chemical and Biomolecular Systems, D. L. Beveridge and W. L. Jorgensen, Eds., Ann. NY Acad. Sci., 482:166-178, 1986.

67.     "Crystallization and Preliminary X-ray Study of AMP Nucleosidase", V. L. Giranda, H. M. Berman, and V. L. Schramm, J. Biol. Chem., 261:15307-15309, 1986.

68.     "Nucleic Acid Hydration:  A Case Study", H. M. Berman, Trans. of American Crystallographic Association, 22:107-119, 1986.

69.     "How Eco RI Recognizes and Cuts DNA", H. M. Berman, Science, 234:1482-1483, 1986.

70.     "Structure of a rearrangement product 1-methyl-3-(5-amino-1-benzylimidazol-4-yl)-1,2,4-triazole, C13H14N6", C. Afshar, H. M. Berman, P. Sawzik, L. Lessinger, B. B. Lim, and R. S. Hosmane, J. Cryst. & Spect. Res., 17:533-543, 1987.

71.     "Anatomy of a Molecular Graphics Program: DOCK", R. K. Stodola, W. P. Wood, Jr., F. J. Manion, H. M. Berman, and N. Badler, in Crystallographic Computing 4:  Techniques and New Technologies, (N. W. Isaacs and M. R. Taylor, eds.), Oxford University Press, pp. 223-246, 1988.

72.     "Structural Characteristics of Actinomycin D That Form the Basis for Its Interactions with DNA", H. M. Berman, S. L. Ginell, P. Sawzik, and L. Lessinger in Structure &Expression:  Volume 2:  DNA and Its Drug Complexes, (R. H. Sarma and M. H. Sarma, eds.), Adenine Press, pp. 317-328, 1988.

73.     "The Crystal and Molecular Structure of the Anticancer Drug Actinomycin D - Some Explanations for Its Unusual Properties", S. Ginell, L. Lessinger, and H. M. Berman, Biopolymers,27:843-864,1988.

74.     "A Systematic Study of Patterns of Hydration in Nucleic Acids: (I) Guanine and Cytosine", H. M. Berman, A. Sowri, S. Ginell, and D. Beveridge, J. Biomol. Struc. & Dyn., 5:1101-1110, 1988.

75.     "Crystal Structure of Formycin 5¢-Phosphate:  An Explanation for Its Tight Binding to AMP Nucleosidase", V. L. Giranda, H. M. Berman, and V. L. Schramm, Biochemistry, 27:5813-5818, 1988.

76.     "A molecular model for proflavine-DNA intercalation", S. Neidle, L. H. Pearl, P. Herzyk, and H. M. Berman, Nucleic Acids Res., 16:8999-9016, 1988.

77.     "Crystallization and Preliminary X-ray Studies of Human Granulocyte-Macrophage Colony Stimulating Factor", J. M. La Londe, L. Hanna, R. Rattoballi, H. M. Berman, and D. Voet, J. Mol. Biol., 205:783-785, 1989.

78.     "Crystallographic Quaternary Structural Analysis of AMP Nucleosidases from E. coli and Azotobacter vinelandii", V. L. Giranda, H. M. Berman, and V. L. Schramm, J. Biol. Chem., 264:15674-15680, 1989.

79.     "Molecular Dynamics Simulation of a Deoxydinucleoside Drug Intercalation Complex:dCpG/Proflavine", S. Swaminathan, D.L. Beveridge and H. M. Berman, J. Phys. Chem., 92:4660-65, 1990.

80.     "A Monte Carlo Simulation Study of the Aqueous Hydration of r(GpC)2: Comparison with Crystallographic Ordered Water Sites", P. S. Subramanian, S. Pitchumani D. L. Beveridge, and H. M. Berman, Biopolymers, 29:771-783, 1990.

81.     "Crystal and Molecular Structure of a DNA Duplex Containing the Carcinogenic Lesion O6-Methylguanine", S. L. Ginell, S. Kuzmich, R.A. Jones, and H. M. Berman, Biochemistry, 29:10461-10465, 1990.

82.     "Crystal and Molecular Structure of a DNA Fragment: d(CGTGAATTCACG) ", N. Narayana, S.L. Ginell, I.M. Russu, and H. M. Berman, Biochemistry,  30:4449-4455, 1991.

83.     "Hydration of DNA", Helen M. Berman, Current Opinion in Structural Biology, 1:423-427, 1991.

84.     "Hydration of DNA Bases: Analysis of Crystallographic Data", B. S. Schneider, D. Cohen, and H. M. Berman, Biopolymers,  32:725-750, 1992.

85.     "The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids", H. M. Berman, W. K. Olson, D. Beveridge, J. Westbrook, A. Gelbin, T. Demeny, S-H. Hsieh, A.R. Srinivasan, and B. Schneider, Biophysical J., 63:751-759, 1992.

86.     "Crystal and Molecular Structure of a DNA Fragment Containing a 2-Aminoadenine Modification:  The Relationship between Conformation, Packing and Hydration in Z-DNA Hexamers", B. Schneider, S. L. Ginell, R. Jones, B. Gaffney, and H. M. Berman, Biochemistry, 31:9622-9628, 1992.

87.     "A Structural Model for Sequence-Specific Proflavin-DNA Interactions During In Vitro Frameshift Mutagenesis", H. M. Berman, J. L. Sussman, L. Joshua-Tor, G. G. Revich, and L. S. Ripley, J. Biomol. Struc. & Dyn., 10:317-331, 1992.

88.     "Low temperature structures of dCpG-proflavine: Conformational and hydration effects", B. Schneider, S. L. Ginell, and H. M. Berman, Biophysical J., 63:1572-1578, 1992.

89.     "Learning to Predict DNA Hydration Patterns", Dawn M. Cohen, Bohdan Schneider, C. Kulikowski and H. M. Berman in Proceedings of the IEEE Conference on AI Applications, IEEE Computer Society Press, pp. 204-210, 1992.

90.     "Hydrogen Bonding in Biological Systems by G.A Jeffrey and W. Saenger", H. M. Berman,Biophysical J., 64, 1993.

91.     "Structure of an Interleukin-1b Mutant with Reduced Bioactivity Shows Multiple Subtle Changes in Conformation that Affect Protein-Protein Recognition", N. P. Camacho, D. R. Smith, A. Goldman, B. Schneider, D. Green, P. R. Young, and H. M. Berman, Biochemistry, 32:8749-8757, 1993.

92.     "Knowledge-Based Generation of Machine Learning Experiments:  Learning DNA Crystallography Data", D. Cohen, C. Kulikowski, and H. M. Berman in Proceedings of the First Intelligent Systems for Molecular Biology  (L. Hunter, D. Searls, and J. Shavlik, eds.) AAAI/MIT Press, pp 92-100, 1993.

93.     "A Systematic Method for Studying the Spatial Distribution of Water Molecules around Nucleic Acid Bases", B. Schneider, D. M. Cohen, L. Schleifer, A. R.Srinivasan, W. K. Olson, and H. M. Berman, Biophysical J., 65:2291-2303, 1993.

94.     "Pt(II) Triamine Complexes: cis-[PtCl(NH3)2(C10H13N5O5)]NO3.2H20 and [PtCl(C2H8N2)(C4H6N2)]NO3", G. M. Arvanitis, D. Gibson, T. J. Emge, and H. M. Berman, Acta Cryst., C50:1217-1220, 1994.

95.     "Crystal Structure and NMR Conformation of a Cyclic Pseudotetrapeptide Containing Urethane Backbone Linkages", G. N. Parkinson, P. Fan, Y. Wu, J. Kohn, J. Baum, and H. M. Berman, Biopolymers, 34:403-414, 1994.

96.     "Ternary Pt(II)-amino acid-nucleotide complexes: kinetics of formation", D. Gibson, G. M. Arvanitis, and H. M. Berman, Inorganica Chimica Acta, 218(1-2):11-19, 1994.

97.     "Crystal Structure of a Mispaired Dodecamer, d(CGAGAATTC(O6Me)GCG)2,Containing a Carcinogenic O6-Methylguanine", S. L. Ginell, J. Vojtechovsky, B. Gaffney, R. Jones, and H. M. Berman, Biochemistry, 33:3487-3493, 1994.

98.     "Analysis of Helix Bending in Crystal Structures and Molecular Dynamics Simulations of DNA Oligonucleotides", M. A. Young, R. Nirmala, J. Srinivasan, K. J. McConnell, G. Ravishanker, D.L. Beveridge, and H. M. Berman, in Structural Biology:  The State of the Art, Volume 2,Adenine Press, 197-214, 1994.

99.     "Hydration of DNA:  take 2", H. M. Berman, Current Opinion in Structural Biology, 4:345-350, 1994.

100.  "Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 Å Resolution", J. Bella, M. Eaton, B. Brodsky, and H. M. Berman, Science, 266:75-81, 1994.

101.  "DEXTER:  A System that Experiments with Choices of Training Data Using Expert Knowledge in the Domain of DNA Hydration", D. M. Cohen, C. Kulikowski, and H. M. Berman, Machine Learning, 21:81-101, 1995.

102.  "Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes", M. A. Young, G. Ravishankar, D.L. Beveridge, and H. M. Berman, Biophysical J., 68:2454-2468, 1995.

103.  "Hydration structure of a collagen peptide", J. Bella, B. Brodsky, and H. M. Berman, Structure, 3:893-906, 1995.

104.  "Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction", N. Spink, C. M. Nunn, J. Vojtechovsky, H. M. Berman, and S. Neidle, Proc. Nat. Acad. Sci., 92:10767-10771, 1995.

105.  "Hydration of the DNA Bases is Local", B. Schneider and H. M. Berman, Biophysical J., 69:2661-2669, 1995.

106.  "Crystal and Molecular Structure of a New Z-DNA Crystal Form:  d[CGT(2-NH2-A)CG] and Its Platinated Derivative", G. Parkinson, G. M. Arvanitis, L. Lessinger, S. L. Ginell, R. Jones, B. Gaffney, and H. M. Berman, Biochemistry, 34:15487-15495, 1995.

107.  "Structure of a New Crystal Form of a DNA Dodecamer Containing T•(O 6Me)G Base Pairs", J. Vojtechovsky, M. D. Eaton, B. Gaffney, R. Jones, and H. M. Berman, Biochemistry, 34:16632-16640, 1995.

108.  "New Parameters for the Refinement of Nucleic Acid-Containing Structures", G. Parkinson, J. Vojtechovsky, L. Clowney, A. T. Brünger, and H. M. Berman, Acta Cryst., D52:57-64, 1996.

109.  "Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents", A. Gelbin, B. Schneider, L. Clowney, F. Huang, W. K. Olson, and H. M. Berman, J. Am. Chem. Soc., 118:519-529, 1996. 

110.  "Geometric Parameters in Nucleic Acids:  Nitrogenous Bases", L. Clowney, S. C. Jain,  A. R. Srinivasan, J. Westbrook, W. K. Olson, and H. M. Berman, J. Am. Chem. Soc., 118:509-518, 1996.

111.  "The Nucleic Acid Database Project", H. M. Berman, D. L. Beveridge, S. Neidle, W. K. Olson, J. Westbrook, A. Gelbin, S-H. Hsieh, L. Clowney, B. Schneider, and C. Zardecki, Biological Structure and Dynamics, Proceedings of the Ninth Conversation of Biomolecular Stereodynamics, Albany, NY, pages 1-13, 1996.

112.  "The Nucleic Acid Database: Present and Future", H. M. Berman, A. Gelbin, L. Clowney, 
S-H. Hsieh, C. Zardecki, and J. Westbrook, J. Res. Natl. Inst. Stand. Technol., 101(03):243-257, 1996.

113.  "Structure of the CAP-DNA Complex At 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface", G. Parkinson, C. Wilson, A. Gunasekera, Y. Ebright, R. H. Ebright, and H. M. Berman, J. Mol. Biol., 260:395-408, 1996.

114.  "Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR", E. Martínez-Hackert, S. Harlocker, M. Inouye, H. M. Berman, and A. M. Stock, Protein Science, 5:1429-1433, 1996.

115.  "Disrupted Collagen Architechture in the Crystal Structure of a Triple-Helical Peptide with a Gly ®Ala Substitution", J. Bella, B. Brodsky, and H. M. Berman, Connective Tissue Research, 35:401-406, 1996.

116.  "Crystallographic Evidence for Ca-H...O=C Hydrogen Bonds in a Collagen Triple Helix", J. Bella and H. M. Berman, J. Mol. Biol., 264:734-742, 1996.

117.  "Aromatic hydrogen bond in sequence-specific protein-DNA recognition", G. Parkinson, A. Gunasekera, J. Vojtechovsky, X. Zhang, T. A. Kunkel, H. M. Berman, and R. H. Elbright, Nat. Struc. Biol., 3:837-841, 1996.

118.  "Nucleic Acid Crystallography:  A View from the Nucleic Acid Database", H. M. Berman, A. Gelbin, and J. Westbrook, Prog. Biophys. Molec. Biol., 66:255-288, 1996.

119.  "The Network Interface to the Nucleic Acid Database", H. M. Berman, L. Clowney, A. Gelbin, C. Zardecki, and J. D. Westbrook, Proceedings: Macromolecular Crystallography Computing School,  Western Washington University, August 17-23, 1996, p.271-285, (San Diego Supercomputer Center, Eds.), 1996.

120.  "Macromolecular Crystallographic Information File", P. Bourne, H. M. Berman, B.  McMahon, K. Watenpaugh, J. D. Westbrook, and P. Fitzgerald, Methods in Enzymology, 277:571-590, 1997.

121.  "Crystal Studies of B-DNA:  The Answers and the Questions", H. M. Berman,Nucleic Acid Sciences, 44:23-44, 1997.

122.  "Conformations of the Sugar-Phosphate Backbone in Helical DNA Crystal Structures", B. Schneider, S. Neidle, and H. M. Berman, Biopolymers, 42:113-124, 1997.

123.  "Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein", J. Liu, P. A. Lynch, C-ya. Chien, G. T. Montelione, R. M. Krug, and H. M. Berman, Nat. Struc. Biol., 4:896-899, 1997.

124.  "X-Ray Crystallographic Determination of a Collagen-like Peptide With the Repeating Sequence (Pro-Pro-Gly)", R. Z. Kramer, L. Vitagliano, J. Bella, R. Berisio, L. Mazzarella, B. Brodsky, A. Zagari, and H. M. Berman, J. Mol. Biol., 280:623-638, 1998.

125.  "The Nucleic Acid Database: A Resource for Nucleic Acid Science", H.M. Berman, C. Zardecki, and J. Westbrook, Acta Cryst., D54:1095-1104, 1998.

126.  "An Analysis of the Relationship between Hydration and Protein-DNA Interactions", J. Woda, B. Schneider, K. Patel, K. Mistry, and H. M. Berman, Biophysical J., 75:2170-2177, 1998.

127.  "Hydration of the Phosphate Group in Double-Helical DNA", B. Schneider, K. Patel, and H. M. Berman, Biophysical J., 75:2422-2434, 1998.

128.  "The Crystal Structure of an Autoprocessed Ser221Cys-subtilisin E-propeptide Complex at 2.0 Å Resolution", S. C. Jain, U. Shinde, Y. Li, M. Inouye, and H. M. Berman, J. Mol. Biol., 284:137-144, 1998.

129.  "Patterns of Hydration In Crystalline Collagen Peptides", R. Z. Kramer and H. M. Berman, J. Biomol. Struct. Dyn., 16:367-380, 1998.

130.  "Maximum A Posteriori Classification of DNA Structure from Sequence Information", D. M. Loewenstern, H.M. Berman, and H. Hirsh, Pac. Symp. Biocomput., 4:669-680, 1998.

131.  "The past and the future of structure databases", H. M. Berman, Curr. Opin. Biotechnol., 10:76-80, 1999.

132.  "CIF Applications. XI. À la Mode: a Ligand and Monomer Object Data Environment I. Automated construction of mmCIF monomer and ligand models", L. Clowney, J. Westbrook, and H. M. Berman, J. Appl. Crystallogr.,  32:125-133, 1999.

133.  "The Nucleic Acid Database: a research and teaching tool", H. M. Berman, C. Zardecki, and J. Westbrook, in Handbook of Nucleic Acid Structure  (ed. S. Neidle) Oxford University Press, pp.77-92, 1999.

134.  "Nucleic acid hydration", H. M. Berman and B. Schneider, in Handbook of Nucleic Acid Structure (ed. S. Neidle) Oxford University Press, pp.295-310, 1999.

135.  "Protein-DNA Interactions: A Structural Analysis", S. Jones, P. van Heyningen, H. M. Berman, and J. M. Thornton, J. Mol. Biol., 287:877-896, 1999.

136.  "Sequence dependent conformational variations of collagen triple-helical structure", R. Z. Kramer, J. Bella, P. Mayville, B. Brodsky, and H. M. Berman, Nat. Struct. Biol., 6:5, 1999.

137.  "Water-Mediation of Hydrogen Bonds in Collagen Triple-Helical Structure", H. M. Berman and R. Z. Kramer, in Perspectives in Structural Biology  (eds. M. Vijayan, N. Yathindra, A.S. Kolaskar) Universities Press, 14:169-178, 1999.

138.  "The Protein Data Bank", H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, Nucleic Acids Research, 28:235-242, 2000.

139.  "An overview of the structures of protein-DNA complexes", N. M. Luscombe, S. E. Austin, H. M. Berman, and J. M. Thornton, Genome Biology, 1(1): 1-37, 2000.

140.  "Integrin-collagen complex: a metal-glutamate handshake", J. Bella and H.M. Berman, Structure, 8:R121-R126, 2000.

141.  "The Protein Data Bank and the challenge of structural genomics", Helen M. Berman, T.N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Helge Weissig, & John Westbrook, Nat. Struct. Biol., 7:957-959, 2000.

142.  "Staggered Molecular Packing of a Collagen-like Peptide With a Single Charged Pair", R.Z. Kramer, M. Venugopal, J. Bella, P. Mayville, B. Brodsky, and H.M. Berman, J. Mol. Biol., 301:1191-1205, 2000.

143.  "Quality controls in databanks for molecular biology", E.E. Abola, A. Bairoch, W.C. Barker, S. Beck, D.A. Benson, H. Berman, G. Cameron, C. Cantor, S. Doubet, T.J.P. Hubbard, T.A. Jones, G.J. Kleywegt, A.S. Kolaskar, A. Van Kuik, A.M. Lesk, H.W. Mewes, D. Neuhaus, F. Pfeiffer, L.F. TenEyck, R.J. Simpson, G. Stoesser, J.L. Sussman, Y. Tateno, A. Tsugita, E.L. Ulrich, J.F.G. Vliegenthart, BioEssays, 22:1024-1034, 2000.

144.  "X-ray Structures of Nucleic Acids", H. Berman, in Encyclopedia of Analytical Chemistry (ed. R.A. Meyers) John Wiley & Sons, Chichester, 6:5285-5298, 2000.

145.  "The PDB data uniformity project", T.N. Bhat, Philip Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider, Kata Schneider, Narmada Thanki, Helge Weissig, John Westbrook and Helen M. Berman, Nucleic Acids Research, 29:214-218, 2001.

146.  "Protein-RNA interactions: a structural analysis", Susan Jones, David T. A. Daley, Nicholas M. Luscombe, Helen M. Berman, and Janet M. Thornton, Nucleic Acids Research, 29:943-954, 2001.

147.  "Checking nucleic acid crystal structures", U. Das, S. Chen, M. Fuxreiter, A. A. Vaguine, J. Richelle, H. M. Berman & S. J. Wodak, Acta Cryst., D57:813-828, 2001.

148.  "The Protein Data Bank, 1999-", Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E., in International Tables for Crystallography (eds. Rossmann, M.G. and Arnold, E.) Vol. F. Crystallography of Biological Macromolecules, Kluwer Academic Publishers, Dordrecht, pp. 675-681, 2001.

149.  "The Nucleic Acid Database (NDB)", Berman, H.M., Feng, Z., Schneider, B., Westbrook, J. and Zardecki, C., in International Tables for Crystallography(eds. Rossmann, M.G. and Arnold, E.) Vol. F. Crystallography of Biological Macromolecules, Kluwer Academic Publishers, Dordrecht, pp. 657-662, 2001.

150.  "The Crystal and Molecular Structure of a Collagen-like Peptide with a Biologically Relevant Sequence", Rachel Z. Kramer, Jordi Bella, Barbara Brodsky, Helen M. Berman, J. Mol. Biol., 311:131-147, 2001.

151.  "Nomenclature: A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry", Wilma K. Olson, Manju Bansal, Stephen K. Burley, Richard E. Dickerson, Mark Gerstein, Stephen C. Harvey, Udo Heinemann, Xiang-Jun Lu, Stephen Neidle, Zippora Shakked, Heinz Sklenar, Masashi Suzuki, Chang-Shung Tung, Eric Westhof, Cynthia Wolberger, Helen M. Berman, J. Mol. Biol., 313:229-237, 2001.

152.  "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking", S. Chen, J. Vojtechovsky, G.N. Parkinson, R.H. Ebright, and H.M. Berman, J. Mol. Biol., 314:63-74, 2001.

153.  "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", S. Chen, A. Gunasekera, X. Zhang, T.A. Kunkel, R.H. Ebright, and H.M. Berman J. Mol. Biol., 314:75-82, 2001.

154.  "The Protein Data Bank: unifying the archive", John Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary L. Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne and Helen M. Berman, Nucleic Acids Research, 30:245-248, 2002.

155.  "The Nucleic Acid Database", H. M. Berman, J. Westbrook, Z. Feng, L. Iype, B. Schneider and C. Zardecki., Acta Cryst., D58:889-898, 2002.

156.  "The Protein Data Bank", 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, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. D. Westbrook and C. Zardecki, Acta Cryst., D58:899-907, 2002.

157.  "Protein Structures: From Famine to Feast", Helen M. Berman, David S. Goodsell and Philip E. Bourne, American Scientist, 90:350 - 359, 2002.

158.  "The CCPN project: an interim report on a data model for the NMR community", Rasmus Fogh, John Ionides, Eldon Ulrich, Wayne Boucher, Wim Vranken, Jens P. Linge, Michael Habeck, Wolfgang Rieping, T.N. Bhat, John Westbrook, Kim Henrick, Gary Gilliland, Helen Berman, Janet Thornton, Michael Nilges, John Markley & Ernest Laue, Nat. Struct. Biol., 9(6):416-418, 2002.

159.  "Structural Basis of Transcription Activation: The CAP-aCTD-DNA Complex", Brian Benoff, Huanwang Yang, Catherine L. Lawson, Gary Parkinson, Jinsong Liu, Erich Blatter, Yon W. Ebright, Helen M. Berman and Richard H. Ebright, Science, 297:1562-1566, 2002.

160.  "The Protein Data Bank and structural genomics", John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman, Nucleic Acids Research, 31:489-491, 2003.

161.  "The Nucleic Acid Database", Berman, H.M., Westbrook, J., Feng, Z., Iype, L., Schneider, B., Zardecki, C., in Structural Bioinformatics (eds. P.E. Bourne and H. Weissig) John Wiley & Sons, Inc., pp. 119-216, 2003.

162.  "Fundamentals of DNA and RNA Structure", Neidle, S., Schneider, B., Berman, H.M., in Structural Bioinformatics(eds. P.E. Bourne and H. Weissig) John Wiley & Sons, Inc., pp. 41-73, 2003.

163.  "The Protein Data Bank", The PDB Team, in Structural Bioinformatics (eds. P.E. Bourne and H. Weissig) John Wiley & Sons, Inc., pp. 181-198, 2003.

164.  "Introduction to Macromolecular Crystallography by A. McPherson" Helen M. Berman, Biochemistry and Molecular Biology Education, 31(2):155-157, 2003.

165.  "The Protein Data Bank", Helen M. Berman, John Westbrook, Christine Zardecki and Philip E. Bourne in Protein Structure: Determination, Analysis, and Applications for Drug Discovery (ed. Daniel I. Chasman), p. 389-405, 2003.

166.  "The Many Twists of DNA", Helen M. Berman and Wilma K. Olson in DNA 50: The Secret of Life (editor M. Balaban) Faircount, London, pp. 104-124, 2003.

167.  "Statistical Models for Discerning Protein Structures Containing the DNA-Binding Helix-Turn-Helix Motif", William A. McLaughlin, Helen M. Berman, Journal of Molecular Biology, 330(1):43-55, 2003.

168.  "Tools for the Automatic Identification and Classification of RNA Base Pairs", Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John Westbrook, Helen Berman, Eric Westhof, Nucleic Acid Research, 31(13):3450-3460, 2003.

169.  "The need for dictionaries, ontologies, and controlled vocabularies", H.M. Berman & J. Westbrook, OMICS, 7:9-10, 2003.

170.  "Announcing the worldwide Protein Data Bank", Helen Berman, Kim Henrick & Haruki Nakamura, Nature Structural Biology, 10(12):980, 2003.

171.   "Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins", Susan Jones, Hugh P. Shanahan, Helen M. Berman, Janet M. Thornton,Nucleic Acids Research, 31:7189-7198, 2003.

172.   "Structural Databases of Biological Macromolecules", Helen M. Berman, in Encyclopedia of the Human Genome (ed. D. N. Cooper), Nature Publishing Group, 5:406-412, 2003.

173.  "Validation Of Protein Structures For The Protein Data Bank", John Westbrook, Zukang Feng, Kyle Burkhardt and Helen M. Berman, in Methods in Enzymology, 374:370-385, 2003.

174.  "The Distribution and Query Systems of the RCSB Protein Data Bank", Philip E. 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 and Helen M. Berman, Nucleic Acid Research, 32:D223-225, 2004.

175.  "The Protein Data Bank: A case study in management of community data", Helen M. Berman, Philip E. Bourne and John Westbrook, Current Proteomics, 1:49-57, 2004.

176.  "Catabolite activator protein (CAP): DNA binding and transcription activation", Catherine L. Lawson, David Swigon, Katsuhiko S. Murakami, Seth A. Darst, Helen M. Berman, and Richard H. Ebright, Current Opinion in Structural Biology, 14(1):10-20, 2004.

177.  "The Protein Data Bank and Lessons in Data Management", Philip E. Bourne, John Westbrook and Helen M. Berman, Journal Briefings in Bioinformatics, 5(1):23-30, 2004.

178.  "RNA conformational classes", Bohdan Schneider, Zdeněk Morávek, and Helen M. Berman, Nucleic Acid Research, 32(5):1666-1677, 2004.

179.  "Ligand Depot: A Data Warehouse for Ligands Bound to Macromolecules", Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, John Westbrook and Helen M. Berman, Bioinformatics, 20:2153-2155, 2004.

180.   "TargetDB: a target registration database for structural genomics projects", Li Chen, Rose Oughtred, Helen M. Berman, and John Westbrook, Bioinformatics, 20:2860-2862, 2004.

181.   "E. coli trp Repressor Forms a Domain-Swapped Array in Aqueous Alcohol", Catherine L. Lawson, Brian Benoff, Tatyana Berger, Helen M. Berman, and Jannette Carey, Structure, 5:1098-1107, 2004.

182.  "Book Review on Protein Crystallography in Drug Discovery," Helen M. Berman, Biochemistry and Molecular Biology Education, 32: 285-286, 2004.

183.  "The Impact of Structural Genomics on the Protein Data Bank", Helen Berman and John D. Westbrook, American Journal of PharmacoGenomics, 4(4): 247-252, 2004.

184.  "Automated and Accurate Deposition of Structures Solved by X-ray Diffraction to the Protein Data Bank," Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman and John Westbrook, Acta Cryst, D60 (10): 1833-1839, 2004.

185.  Helen M. Berman, interview by David N. Berol at New Brunswick, New Jersey, 11 February 2000 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0191)

186.  "A Structure-based Method for Identifying DNA-Binding Proteins and their sites of DNA-Interaction," William McLaughlin, Joanna de la Cruz, Xiang-Jun Lu, Catherine L. Lawson and Helen M. Berman, Journal of Structural and Functional Genomics, 5(4): 255-265, 2004.

187.  "PDBML: The representation of archival macromolecular structure data in XML," John Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman, Bioinformatics, 21(7): 988-992, 2005.

188.  "The RCSB Protein Data Bank: A Redesigned Query System and Relational Database Based on the mmCIF Schema," Nita Deshpande, Kenneth J. Addess, Wolfgang F. Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John Westbrook, Helen M. Berman and Philip E. Bourne, Nucl. Acids Res. 33: D233-D237, 2005.

189.   "Design of a data model for developing laboratory information management and analysis systems for protein production," 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. Proteins: Structure, Function, and Bioinformatics, 58(2): 278-284, 2005.

190.  "The Cyclic Adenosine Monophosphate Binding Domain: An Ancient Signaling Module," Helen M. Berman, Lynn Ten Eyck, David S. Goodsell, Nina Haste, Alexandr Kornev and Susan Taylor, Proceedings of the National Academy of Science, 102:45-50, 2005. PMCID: PMC544069.

191.  "Large Macromolecular Complexes in the Protein Data Bank: A Status Report," Shuchismita Dutta and Helen M. Berman, Structure, 13(3): 381-388, 2005.

192.  "Using the Tools and Resources of the RCSB Protein Data Bank," Shuchismita Dutta, Kyle Burkhardt, Wolfgang F. Bluhm, and Helen M. Berman, Current Protocols in Bioinformatics, 1.9.1-1.9.40, 2005. 

193.  "Macromolecular dictionary (mmCIF)", P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh, and H. M. Berman, in International Tables for Crystallography (eds. S. Hall and B. McMahon) Vol. G Definition and exchange of crystallographic data, Springer, Dordrecht, The Netherlands, 295-443, 2005.

194.  "Classification and use of macromolecular data", P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh, and H. M. Berman, in International Tables for Crystallography (eds. S. Hall and B. McMahon) Vol. G Definition and exchange of crystallographic data, Springer, Dordrecht, The Netherlands, 144-198, 2005.

195.  "The use of mmCIF architecture for PDB data management" J. D. Westbrook, H.Yang, Z. Feng and H. M. Berman, in International Tables for Crystallography (eds. S. Hall and B. McMahon) Vol. G Definition and exchange of crystallographic data, Springer, Dordrecht, The Netherlands, 539-543, 2005.

196.  "The Protein Data Bank Exchange Data Dictionary" J. D. Westbrook, K. Henrick, E. L. Ulrich and H.M. Berman, in International Tables for Crystallography (eds. S. Hall and B. McMahon) Vol. G Definition and exchange of crystallographic data, Springer, Dordrecht, The Netherlands, 195-198, 2005.

197.  "Specification of a relational dictionary definition language (DDL2)", J. D. Westbrook, H.M. Berman and S.R. Hall, in International Tables for Crystallography (eds. S. Hall and B. McMahon) Vol. G Definition and exchange of crystallographic data, Springer, Dordrecht, The Netherlands, 61-72, 2005.

198.  "Ontologies for three-dimensional molecular structure", John Westbrook and Helen M. Berman, Encyclopedia of Genomics, Proteomics and Bioinformatics, Jorde, L.B., Little, P.F.R., Dunn, M.J. and Subramaniam, S. (Eds), John Wiley & Sons Ltd: Chichester, vol 8, 3474-3480, 2005.

199.   "The Protein Data Bank and the wwPDB", Kim Henrick, Helen M. Berman and Haruki Nakamura, Encyclopedia of Genomic, Proteomic and Bioinformatics, Jorde, L.B., Little, P.F.R., Dunn, M.J. and Subramaniam, S. (Eds), John Wiley & Sons Ltd: Chichester, vol 7, 3335-3339, 2005.

200.   "The RCSB PDB Information Portal for Structural Genomics," Andrei Kouranov, Lei Xie, Joanna de la Crux, Li Chen, John Westbrook, Philip Bourne and Helen Berman, Nucleic Acids Research, Vol 34, Database issue: D302-D305, 2006.

201.   "Is one solution good enough? (response)," Helen M. Berman, Kim Henrick, Haruki Nakamura, Eddy Arnold, Nature Structural and Molecular Biology, 13:185, 2006.

202."Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps", Napoli, A. A., Lawson, C. L., Ebright, R. H., Berman, H. M., J. Mol. Biol, 357:173-183, 2006.

203.   "Reflections on the Science and Law of Structural Biology, Genomics, & Drug Development", Helen M. Berman, Rochelle C. Dreyfuss, UCLA Law Review,53: 871-908, 2006.

204.   "The RNA Ontology Consortium: An open invitation to the RNA community", Neocles B. Leontis, Russ B. Altman, Helen M. Berman, Steven E. Brenner, James W. Brown, David R. Engelke, Stephen C. Harvey, Sephen R. Holbrook, Fabrice Jossinet, Suzanna E. Lewis, Francois Major, David H. Mathews, Jane S. Richardson, James R Williamson, and Eric Westhof, RNA, 12(4):  533-541, 2006. 

205.   "Basics of Nucleic Acid Structure. Concepts, Tools, and Archives", Bohdan Schneider and Helen M. Berman, in Computational approaches to nucleic acid structures, (eds. J. Sponer and F. Lankas), Springer, Berlin, Germany, 1-44, 2006.

206.   "Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules", Helen M. Berman, Stephen K. Burley, Wah Chiu, Andrej Sali, Alexei Adzhubei, Philip E. Bourne, Stephen H. Bryant, Roland L. Dunbrack, Jr., Krzysztof Fidelis, Joachim Frank, Adam Godzik, Kim Henrick, Andrzej Joachimiak, Bernard Heymann, David Jones, John L. Markley, John Moult, Gaetano T. Montelione, Christine Orengo, Michael G. Rossmann, Burkhard Rost, Helen Saibil, Torsten Schwede, Daron M. Standley, John D. Westbrook, Structure, 14(8):1211-1217, 2006.

207.   "Conformational Effects of Gly-X-Gly Interruptions in the Collagen Triple Helix", Jordi Bella, Jingsong Liu, Rachel Kramer, Barbara Brodsky, and Helen M. Berman, Journal of Molecular Biology, 362(2): 298-311, 2006.

208.   "The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data",  Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley, Nucleic Acids Res., 35 (Database issue): D301-3, 2007.

209.   "The Research Collaboratory for Structural Bioinformatics Protein Data Bank", P. Bourne, W. F. Bluhm, N. Deshpande, Q. Zhang, H. M. Berman and J. L. Flippen-Anderson, Comprehensive Medicinal Chemistry II, Vol. 3, Drug Discovery Technologies, pp.373-388, 2007.


210.  "Reply to: Building meaningful models of glycoproteins", Helen M. Berman, Kim Henrick, Haruki Nakamura and John Markley, Nat Struct Mol Biol, 14:354-355, 2007.


211.  "Realism about PDB", Helen M. Berman, Kim Henrick, Haruki Nakamura, John Markley, Philip E. Bourne, and John Westbrook, Nature Biotechnology, 25:845-846, 2007.


212. "Using RCSB PDB Tools and Resources," Shuchismita Dutta, Helen M. Berman, and Wolfgang F. Bluhm,  Current Protocols in Bioinformatics, 1.9.1-1.9.24, DOI: 10.1002/0471250953.bi0109s20, 2007.


213. "Remediation of the Protein Data Bank Archive", K. Henrick, Z. Feng, W. Bluhm, D. Dimitropoulos, J.F. Doreleijers, S. Dutta, J.L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C.L. Lawson, J.L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E.L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin, and H. Berman, Nucleic Acids Res., 36(Database issue): D426-D433, 2008.


214."The Protein Data Bank: a historical perspective", H. M. Berman, Acta Cryst., A64:88-95, 2008.


215.  "RNA backbone:  Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)", Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. 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, and Helen M. Berman, RNA, 14:465-481, DOI: 10.1261/rna.657708, 2008.

216.  "Harnessing Knowledge from Structural Genomics", Helen M. Berman, Structure, 16:16-18, 2008.

217.   "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions", John L. Markley, Eldon L. Ulrich, Helen M. Berman, Kim Henrick, Haruki Nakamura, and Hideo Akutsu, Journal of Biomolecular NMR, 40:153-155, 2008.


218.  "Data deposition and annotation at the Worldwide Protein Data Bank", Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, and Helen M. Berman, in Methods in Molecular Biology, vol. 426: Structural Proteomics: High-Throughput Methods (Bostjan Kobe, Mitchell Guss, Thomas Huber, eds.), pp. 81-101, 2008.


219.  "Indirect readout of DNA sequence by proteins, in Protein-Nucleic Acid Interactions" C.L. Lawson and H.M. Berman, Chapter 4: P.A. Rice and C.C. Correll, Editors. Royal Society of Chemistry: Cambridge, UK, 66-90, 2008.


220.  "Representation of viruses in the remediated PDB archive" C. L. Lawson, S. Dutta, J. D. Westbrook, K. Henrick, and H. M. Berman, Acta Cryst, D64, 874-882  [DOI: 10.1107/S0907444908017393], 2008.


221.  "The Protein Model Portal" K. Arnold, F. Kiefer, J. Kopp, J.N. Battey, M. Podvinec, J. Westbrook, H.M. Berman, L. Bordoli, and T. Schwede, Journal of Structural and Functional Genomics, Volume 10, Issue 1, 1-8, 2009.


222.  "The Protein Structure Initiative Structural Genomics Knowledgebase" H.M. Berman, J.D. Westbrook, M.J. Gabanyi, Y. Tao, R. Shah, A. Kouranov, T. Schwede, K. Arnold, F. Kiefer, L. Bordoli, J. Kopp, M. Podvinec, P.D. Adams, L.G. Carter, W. Minor, R. Nair, and J. La Baer, Nucleic Acids Research, Vol. 37, Database issue D365-D368, 2009.


223.  "Signatures of protein-DNA recognition in free DNA binding sites" J.W. Locasale, A. A. Napoli, S. Chen, H.M. Berman, and C. L. Lawson, J Mol Biol., 386, 1054-1065, 2009. PMCID: PMC2753591.


224.  "Outcome of a Workshop on Applications of Protein Models in Biomedical Research" T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D.T. Jones, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack, Jr., K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R.K. Jr., T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, and I.A. Wilson, Structure, Volume 17, Issue 2, 151-159, 2009.


225.  "The Worldwide Protein Data Bank" H.M. Berman, K. Henrick, H. Nakamura, and J.L. Markley, in Structural Bioinformatics, 2nd. Edition, P.E. Bourne and J. Gu, Editors, John Wiley & Sons, Inc.: Hoboken, NJ, 293-303, 2009.


226.  "Fundamentals of DNA and RNA structure" S. Neidle, B. Schneider, and H.M. Berman, in Structural Bioinformatics, 2nd. Edition,P.E. Bourne and J. Gu, Editors, John Wiley & Sons, Inc.: Hoboken, NJ, 41-76, 2009.


227.  "The Nucleic Acid Database" B. Schneider, J. de la Cruz, Z. Feng, L. Chen, S. Dutta, I. Persikova, J. D. Westbrook, H. Yang, J. Young, C. Zardecki, and H.M. Berman, in Structural Bioinformatics, 2nd. Edition, P.E. Bourne and J. Gu, Editors, John Wiley & Sons, Inc.: Hoboken, NJ, 305-319, 2009.


228.  "Data deposition and annotation at the Worldwide Protein Data Bank" S. Dutta, K. Burkhardt, J. Young, G.J. Swaminathan, T. Matsuura, K. Henrick, H. Nakamura, and H.M. Berman, Molecular Biotechnology,42:1-13, 2009.


229.  "Three-dimensional EM Structure of an Intact Activator-Dependent Transcription Initiation Complex" B.P. Hudson, J. Quispe, S. Lara, Y. Kim, H.M. Berman, E. Arnold, R.H. Ebright, Proceedings of the National Academy of Sciences, 106:19830-19835, 2009, doi: 10.1073/pnas.0908782106. PMCID PMC2775702.

230.   "Safeguarding the integrity of the protein archive"H.M. Berman, G.J. Kleywegt, H. Nakamura, J.L. Markley, S.K. Burley, Nature 463: 425, 2010. 


231.  "Promoting a Structural View of Biology for Varied Audiences: An Overview of RCSB PDB Resources and Experiences" Shuchismita Dutta,  Christine Zardecki,  David S. Goodsell and  Helen M. Berman, Journal of Applied Crystallography, 43:1224-1229, 2010, doi: 10.1107/S002188981002371X.


232.  "Workshop on the Validation and Modeling of Electron Cryo-Microscopy Structures of Biological Nanomachines - Workshop Introduction" S.J. Ludtke, C.L. Lawson, G.J. Kleywegt, H.M. Berman, W. Chiu, Pac Symp Biocomput. 369-73, 2011.


233.  " unified data resource for CryoEM" C.L. Lawson, M.L. Baker, C. Best, C. Bi, M. Dougherty, P. Feng, G. van Ginkel, B. Devkota, I. Lagerstedt, S.J. Ludtke, R.H. Newman, T.J. Oldfield, I. Rees, G. Sahni, R. Sala, S. Velankar, J. Warren, J.D. Westbrook, K. Henrick, G.J. Kleywegt, H.M. Berman, W. Chiu, Nucleic Acids Res. 39:D456-D4642011, doi: 10.1093/nar/gkq880. PMCID: PMC3013769.


234.  "The RCSB Protein Data Bank: redesigned web site and web services" Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang F. Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlić, Martha Quesada, Gregory B. Quinn, John D. Westbrook, Jasmine Young, Benjamin Yukich, Christine Zardecki, Helen M. Berman, Philip E. Bourne, Nucleic Acids Res. 39: D392-D4012011, doi: 10.1093/nar/gkq1021.


235.  "Quality Assurance for the Query and Distribution Systems of the RCSB Protein Data Bank" Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlić, Gregory B. Quinn, Peter W. Rose, Chaitali Shah, Ben Yukich, Helen M. Berman, Philip E. Bourne, Database, 2011, doi: 10.1093/database/bar003.


236.  "The RCSB Protein Data Bank: site functionality and bioinformatics use cases" Peter W. Rose, Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlić, Gregory B. Quinn, Benjamin Yukich, Helen M. Berman, Philip E. Bourne, NCI-Nature Pathway Interaction Database Bioinformatics Primer, 2011, doi: 10.1038/pid.2011.1.


237.   "The Structural Biology Knowledgebase: A portal to protein structures, sequences, functions, and methods" Margaret J. Gabanyi, Paul D. Adams, Konstantin Arnold, Lorenza Bordoli, Lester G. Carter, Judith Flippen-Anderson, Lida Gifford, Juergen Haas, Andrei Kouranov, William A. McLaughlin, David I. Micallef, Wladek Minor, Raship Shah, Torsten Schwede, Yi-Ping W. Tao, John D. Westbrook, Matthew Zimmerman, Helen M. Berman, Journal of Structural and Functional Genomics 12:45-54, 2011, doi: 10.1007/s10969-011-9106-2.


238.  "The Evolution of the RCSB Protein Data Bank Website" Boki Beran, Chunxiao Bi, Wolfgang F. Bluhm, Dimitris Dimitropoulos, Zukang Feng, David S. Goodsell, Andreas Prlic, Gregory Quinn, Peter Rose, John Westbrook, Ben Yukich, Jasmine Young, Christine Zardecki, Helen M. Berman, WIREs Computational Molecular Science, 2011, doi: 10.1002/wcms.57.


239.   "Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction"  A. Kryshtafovych, S. Bartual, J.F. Bazan, H.M. Berman, D. Casteel, E. Christodoulou, J. Everett, J. Hausmann, T. Heidebrecht, T. Hills, R. Hui, J. Hunt, S. Jayaramanand, A. Joachimiak, M. Kennedy, C. Kim, A. Lingel, K. Michalska, G. Montelione, J. Otero, A. Perrakis, J. Pizarro, M.J. vanRaaij, T. Ramelot, F. Rousseau, A. Wernimont, J. Young, T. Schwede, PROTEINS: Structure, Function, and Bioinformatics, 79: 6-20, 2011 doi: 10.1002/prot.23196.


240.   "Celebrating structural biology" Tom L. Blundell, Stephen C. Harrison, Robert M. Stroud, Shigeyuki Yokoyama, Lewis E. Kay, Michael G. Rossmann, Helen M. Berman, Alexander Wlodawer, Elena Conti, Brian Kobilka, Janet M Thornton, David Cowburn, Nenad Ban, Olga Boudker Nature Structural &Molecular Biology 18: 1304-1316, 2011 doi: 10.1038/nsmb1211-1304.


241.   "The Protein Data Bank" Helen M. Berman, Leadership in Science and Technology: A Reference Handbook (William Sims Bainbridge, editor) SAGE Publications, Inc.: Thousand Oaks, CA, volume 2, pages 661-675, 2012. 


242.   "Outcome of the First Electron Microscopy Validation Task Force Meeting" Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, Catherine L. Lawson Structure 20: 205-214, 2012 doi: 10.1016/j.str.2011.12.014.


243.   "The Protein Data Bank at 40: Reflecting on the past to prepare for the future" H.M. Berman, G. Kleywegt, H. Nakamura, J. Markley, Structure, 20: 391-396, 2012 doi: 10.1016/j.str.2012.01.010


244.    "The Nucleic Acid Database" B. Schneider, J. de la Cruz, S. Dutta, Z. Feng, L. Chen, J. Westbrook, H. Yang, J. Young, C. Zardecki, H.M. Berman, in International Tables for X-Ray Crystallography (eds. E. Arnold, D.M. Himmel, M.G. Rossmann) Volume F:  Crystallography of biological macromolecules, Springer, Dordrecht, The Netherlands, ch. 24.2, pp. 833-837, 2012  doi: 10.1107/97809553602060000897.


245.  "The Worldwide Protein Data Bank" H.M. Berman, K. Henrick, G. Kleywegt, H. Nakamura, J. Markley, in International Tables for X-Ray Crystallography (eds. E. Arnold, D.M. Himmel, M.G. Rossmann) Volume F:  Crystallography of biological macromolecules, Springer, Dordrecht, The Netherlands, ch. 24.1, pp. 827-832, 2012  doi:10.1107/97809553602060000896.


246.   "Assessing the quality of macromolecular structures"S.J. Wodak, A.A. Vagin, J. Richelle, U. Das, J. Pontius and H.M. Berman in International Tables for X-Ray Crystallography (eds. E. Arnold, D.M. Himmel, M.G. Rossmann) Volume F:  Crystallography of biological macromolecules, Springer, Dordrecht, The Netherlands, ch. 21.2, pp. 662-676, 2012 doi:10.1107/97809553602060000880.


247.   "The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource" Lida K. Gifford, Lester G. Carter, Margaret J. Gabanyi, Helen M. Berman and Paul D. Adams, Journal of Structural and Functional Genomics,13:57-62, 2012 doi: 10.1007/s10969-012-9133-7.


248.   "The 2010 cryo-em modeling challenge" Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen Berman and Wah Chiu, Biopolymers, 97:651-654, 2012 doi: 10.1002/bip.22081.


249.   "Creating a community resource for protein Science"Helen Berman, Protein Science, 21: 1587-1596, 2011 doi: 10.1002/pro.2154.


250.   "The RCSB Protein Data Bank: New resources for research and education" Peter Rose, Chunxiao Bi, Wolfgang Bluhm, Cole Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel Kramer Green, David Goodsell, Andreas Prlic, Martha Quesada, Greg Quinn, Alexander Ramos, John Westbrook, Jasmine Young, Christine Zardecki, Helen Berman, Philip Bourne,Nucleic Acids Research 41: D475-D482, 2013 [ doi: 10.1093/nar/gks1200 ].


251.   "The Future of the Protein Data Bank" Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley,Biopolymers 99: 218-222, 2013  [ doi: 10.1002/bip.22132 ]


252.   "An overview of structural studies of the collagen triple helix" H. M. Berman, R. Kramer Green in Biomolecular Forms and Functions.  A Celebration of 50 years of the Ramachandran Map, M. Bansal & N. Srinivasan, eds. Singapore: World Scientific Publishing Co. Pte. Ltd., pp. 17-37, 2013.