Helen M. Berman

Bio: Helen M. Berman is an academic researcher from Rutgers University. The author has contributed to research in topics: Protein Data Bank & Protein Data Bank (RCSB PDB). The author has an hindex of 86, co-authored 315 publications receiving 58724 citations. Previous affiliations of Helen M. Berman include Texas A&M University & Temple University.

The Protein Data Bank

Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. 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.

Announcing the worldwide Protein Data Bank.

Abstract: mentation will be kept publicly available and the distribution sites will mirror the PDB archive using identical contents and subdirectory structure. However, each member of the wwPDB will be able to develop its own web site, with a unique view of the primary data, providing a variety of tools and resources for the global community. An Advisory Board consisting of appointees from the wwPDB, the International Union of Crystallography and the International Council on Magnetic Resonance in Biological Systems will provide guidance through annual meetings with the wwPDB consortium. This board is responsible for reviewing and determining policy as well as providing a forum for resolving issues related to the wwPDB. Specific details about the Advisory Board can be found in the wwPDB charter, available on the wwPDB web site. The RCSB is the ‘archive keeper’ of wwPDB. It has sole write access to the PDB archive and control over directory structure and contents, as well as responsibility for distributing new PDB identifiers to all deposition sites. The PDB archive is a collection of flat files in the legacy PDB file format 3 and in the mmCIF 4 format that follows the PDB exchange dictionary (http://deposit.pdb.org/ mmcif/). This dictionary describes the syntax and semantics of PDB data that are processed and exchanged during the process of data annotation. It was designed to provide consistency in data produced in structure laboratories, processed by the wwPDB members and used in bioinformatics applications. The PDB archive does not include the websites, browsers, software and database query engines developed by researchers worldwide. The members of the wwPDB will jointly agree to any modifications or extensions to the PDB exchange dictionary. As data technology progresses, other data formats (such as XML) and delivery methods may be included in the official PDB archive if all the wwPDB members concur on the alteration. Any new formats will follow the naming and description conventions of the PDB exchange dictionary. In addition, the legacy PDB format would not be modified unless there is a compelling reason for a change. Should such a situation occur, all three wwPDB members would have to agree on the changes and give the structural biology community 90 days advance notice. The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform. It provides a mechanism to ensure consistent data for software developers and users worldwide. We hope that this will encourage individual creativity in developing tools for presenting structural data, which could benefit the scientific research community in general.

The Protein Data Bank.

Abstract: The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Abstract: The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. 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.

Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution.

Abstract: The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)n pattern by a Gly-->Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly-->X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.

UCSF Chimera--a visualization system for exploratory research and analysis.

Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

The Protein Data Bank

Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. 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.

Crystal structure refinement with SHELXL

Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

Coot: model-building tools for molecular graphics.

Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.