PDBML: the representation of archival macromolecular structure data in XML

Summary: The Protein Data Bank (PDB) has recently released versionsof the PDB Exchange dictionary and the PDB archival data filesin XML format collectively named PDBML. The automated generationof these XML files is driven by the data dictionary infrastructurein use at the PDB. The correspondences between the PDB dictionaryand the XML schema metadata are described as well as the XMLrepresentations of PDB dictionaries and data files. Availability: The current software translated XML schema fileis located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd,and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/.PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML Contact: jwest{at}rcsb.rutgers.edu     

The PDB data uniformity project

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 data uniformity project that is underway to address the inconsistency in PDB data.     

The Protein Data Bank

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.     

Automated analysis of interatomic contacts in proteins.

MOTIVATION: New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein. RESULTS: Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues. Our approach is based on a detailed analysis of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-accessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of the ligand. AVAILABILITY: Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.     

The Protein Data Bank and structural genomics

The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projects--developing and maintaining the Target Registration Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture data from standard structure determination applications.     

Pre-calculated protein structure alignments at the RCSB PDB website

SUMMARY: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. Availability and Implementation: A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org CONTACT: andreas@sdsc.edu; pbourne@ucsd.edu.     

Proteomics FASTA archive and reference resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.     

Disulfide by Design: a computational method for the rational design of disulfide bonds in proteins

SUMMARY: Disulfide by Design is a program for the design of novel disulfide bonds in proteins. Protein structure files in PDB format are analyzed to identify residue pairs that are likely to form a disulfide bond if the respective amino acids are mutated to cysteines. The output displays residue pairs having the appropriate geometric characteristics for disulfide formation and provides automated generation of modified PDB files including modeled disulfides. Validation demonstrates a high level of accuracy for the algorithm. AVAILABILITY: http://www.ehscenter.org/dbd/ Supplementary information: http://www.ehscenter.org/dbd/     

TMCompare: transmembrane region sequence and structure.

TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions; examination of differences in coverage between PDB and SWISS-PROT files; examination of annotation differences between PDB files and associated SWISS-PROT files; examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format; examination of these differences in 3D using the CHIME plugin, allowing; analysis of the alpha and non-alpha content of transmembrane regions. AVAILABILITY: TMCompare is available for use through selection of a query protein via the internet (http://www.membraneproteins.org/TMCompare) CONTACT: tmcompare@membraneproteins.org     

Drug efficacy of novel 3-O-methoxy-4-halo disubstituted 5,7-dimethoxy chromans; evaluated via DNA gyrase inhibition,bacterial cell wall lesion and antibacterial prospective

In this study, novel 3-O-methoxy-4-halo, disubstituted-5,7-dimethoxy chromans with bacterial cell wall degrading potentials were synthesized, characterized and evaluated as DNA gyrase inhibitors and antibacterial agents. Compounds were showed a broad spectrum of antimicrobial activity against both Gram^+ve bacteria (S. aureus (MTCC 3160), C. diphtheriae (MTCC 116), S. pyogenes (MTCC 442)) and Gram^?ve bacteria (E. coli (MTCC 443), P. aeruginosa (MTCC 424), K. pneumoniae (MTCC 530)). Further, a molecular docking study was carried out to get more insight into the binding mode of present study compounds to target proteins (PDB ID: 2XCT (S. aureus DNA gyrase A), PDB ID: 3G75 (S. aureus DNA gyrase B), PDB ID: 3L7L (Teichoic acid polymerase). In the results, 14?>?20?>?24?>?12?>?18?>?17 were found as the most active against almost all executed activities in this study. The predicted Lipinski’s filter scores, SAR, pharmacokinetic/pharmacodynamics, and ADMET properties of these compounds envisioned the druggability prospects and the necessity of further animal model evaluations of 3-O-methoxy-4-halo disubstituted 5,7-dimethoxy chromans to establish them as an effective and future antibiotics.     

TargetDB: a target registration database for structural genomics projects

TargetDB is a centralized target registration database that includes protein target data from the NIH structural genomics centers and a number of international sites. TargetDB, which is hosted by the Protein Data Bank (RCSB PDB), provides status information on target sequences and tracks their progress through the various stages of protein production and structure determination. A simple search form permits queries based on contributing site, target ID, protein name, sequence, status and other data. The progress of individual targets or entire structural genomics projects may be tracked over time, and target data from all contributing centers may also be downloaded in the XML format. AVAILABILITY: TargetDB is available at http://targetdb.pdb.org/     

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.     

BioDownloader: bioinformatics downloads and updates in a few clicks

There are many ftp or http servers storing data required for biological research. While some download applications are available, there is no user-friendly download application with a graphical interface specifically designed and adapted to meet the requirements of bioinformatics. BioDownloader is a program for downloading and updating files from ftp and http servers. It is optimized to work robustly with large numbers of files. It allows the selective retrieval of only the required files (batch downloads, multiple file masks, ls-lR file parsing, recursive search, recent updates, etc.). BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) databases. It can post-process downloaded files, including archive extraction and file conversions. AVAILABILITY: The program can be installed from http://dunbrack.fccc.edu/BioDownloader. The software is freely available for both non-commercial and commercial users under the BSD license.     

BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of `Magnetic Resonance' (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu).     

DECOMP: A PDB decomposition tool on the web

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi­monomer ligands, and the server also offers the preprocessed ligand­protein decomposition of the complete PDB for downloading (up to size: 5GB)

Availability

http://decomp.pitgroup.org     

PDB2MultiGIF: A Web Tool to Create Animated Images of Molecules

A new web tool, PDB2MultiGIF (http://www.dkfz-heidelberg.de/spec/pdb2mgif/),which converts the topological information (atom types, 3D coordinates, molecular connectivity) of molecules (given in PDB format [1]) to a series of animated images (in GIF Format) [2] is described. The molecular visualisation program RASMOL [3] is used to generate the images.Electronic Supplementary Material available.     

Location of the extrinsic subunit PsbP in photosystem II studied by pulsed electron-electron double resonance

The binding site of the extrinsic protein PsbP in plant photosystem II was mapped by pulsed electron-electron double resonance, using mutant spinach PsbP (Pro20Cys, Ser82Cys, Ala111Cys, and Ala186Cys) labeled with 4-maleimido-TEMPO (MSL) spin label. The distances between the spin label and the Tyr160 neutral radical (Y_D) in PsbD, the D2 subunit of plant photosystem II, were 50.8?±?3.5?Å, 54.9?±?4.0?Å, 57.8?±?4.9?Å, and 58.4?±?14.1?Å, respectively. The geometry inferred from these distances was fitted to the PsbP crystal structure (PDB: 4RTI) to obtain the coordinates of Y_D relative to PsbP. These coordinates were then fitted under boundary conditions to the structure of cyanobacterial photosystem II (PDB: 4UB6), by rotating on Euler angles centered at fixed Y_D coordinates. The result proposed two models which show possible acidic amino acid residues in CP43, CP47 and D2 that can bind the basic amino acids Arg48, Lys143, and Lys160 in PsbP.     

MAPS: an interactive web server for membrane annotation of transmembrane protein structures

The exact positioning of the membrane in transmembrane (TM) proteins plays important functional roles. Yet, the structures of TM proteins in protein data bank (pdb) have no information about the explicit position of the membrane. Using a simple hydrophobic lipid-protein mismatch energy function and a flexible lipid/water boundary, the position of lipid bilayer for representative TM proteins in pdb have been annotated. A web server called MAPS (Membrane Annotation of Protein Structures; available at: http://www.boseinst.ernet.in/gautam/maps) has been set up that allows the user to interactively analyze membrane-protein orientations of any uploaded pdb structure with user-defined membrane flexibility parameters.