OneDep: Unified wwpdb System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Transcription

1 Resource OneDep: Unified wwpdb System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive Highlights d wwpdb has deployed a unified wwpdb OneDep system globally d d wwpdb has improved structure validation using community widely adopted software The processing efficiency in biocuration is improved via more automated workflow Authors Jasmine Y. Young, John D. Westbrook, Zukang Feng,..., Haruki Nakamura, Sameer Velankar, Stephen K. Burley Correspondence jasmine.young@rcsb.org In Brief The worldwide PDB (wwpdb) has developed a unified system, called OneDep, for deposition, biocuration, and validation of macromolecular structures to the PDB to meet the evolving archiving requirements of the scientific community over the coming decades. Young et al., 2017, Structure 25, March 7, 2017 Published by Elsevier Ltd.

2 Structure Resource OneDep: Unified wwpdb System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive Jasmine Y. Young, 1,12, * John D. Westbrook, 1 Zukang Feng, 1 Raul Sala, 1 Ezra Peisach, 1 Thomas J. Oldfield, 2,9 Sanchayita Sen, 2 Aleksandras Gutmanas, 2 David R. Armstrong, 2 John M. Berrisford, 2 Li Chen, 1 Minyu Chen, 3 Luigi Di Costanzo, 1 Dimitris Dimitropoulos, 1,10 Guanghua Gao, 1 Sutapa Ghosh, 1 Swanand Gore, 2 Vladimir Guranovic, 1 Pieter M.S. Hendrickx, 2 Brian P. Hudson, 1 Reiko Igarashi, 3 Yasuyo Ikegawa, 3 Naohiro Kobayashi, 3 Catherine L. Lawson, 1 Yuhe Liang, 1 Steve Mading, 4 Lora Mak, 2 M. Saqib Mir, 2 Abhik Mukhopadhyay, 2 Ardan Patwardhan, 2 Irina Persikova, 1 Luana Rinaldi, 2 Eduardo Sanz-Garcia, 2 Monica R. Sekharan, 1 Chenghua Shao, 1 G. Jawahar Swaminathan, 2,11 Lihua Tan, 1 Eldon L. Ulrich, 4 Glen van Ginkel, 2 Reiko Yamashita, 3 Huanwang Yang, 1 Marina A. Zhuravleva, 1 Martha Quesada, 1 Gerard J. Kleywegt, 2 Helen M. Berman, 1 John L. Markley, 4 Haruki Nakamura, 3 Sameer Velankar, 2 and Stephen K. Burley 1,5,6,7,8 1 RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA 2 Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK 3 PDBj, Institute for Protein Research, Osaka University, Osaka, , Japan 4 BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA 5 RCSB Protein Data Bank, San Diego Supercomputer Center 6 Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego, La Jolla, CA 92093, USA 7 Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA 8 Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA 9 Present address: Dotmatics, The Old Monastery, Windhill, Bishops Stortford, Herts CM23 2ND, UK 10 Present address: Google, Irvine, CA 92612, USA 11 Present address: Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford CB10 1XL, UK 12 Lead Contact *Correspondence: jasmine.young@rcsb.org SUMMARY OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwpdb) partners. This new system was designed to ensure that the wwpdb could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwpdb, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments. INTRODUCTION The PDB, which was established in 1971 with just seven X-ray crystal structures of proteins, became the first open-access digital primary data resource in biology (Protein Data Bank, 1971). Today, the PDB archive serves as the single global repository for more than 120,000 experimentally determined atomic-level structures of biological macromolecules (protein, DNA, RNA) and their complexes. The worldwide PDB (wwpdb) partnership, the international collaboration that manages the PDB archive, supports deposition, biocuration, validation, and distribution of PDB data (Berman et al., 2003). This partnership was established in 2003 by three founding members: Research Collaboratory for Structural Bioinformatics PDB or RCSB PDB (Berman et al., 2000), the PDB in Europe or PDBe (Velankar et al., 2016), and the PDB Japan or PDBj (Kinjo et al., 2012). Subsequently, a specialist nuclear magnetic resonance (NMR) spectroscopic data resource, the Biological Magnetic Resonance Data Bank or BMRB (Ulrich et al., 2008), joined the wwpdb. The mission of the wwpdb organization is to ensure that the PDB archive will continue in perpetuity as a high-quality, open-access digital data resource with no limitations on usage (Berman et al., 2013). The PDB archive has grown substantially during the past 45 years (Figure 1) and now includes structures determined by crystallography (primarily X-ray), NMR spectroscopy, and 3D electron cryomicroscopy (3DEM). The growth of the PDB archive and the increasing complexity of the structures produced by the structural biology community have pushed the limits of 536 Structure 25, , March 7, 2017 Published by Elsevier Ltd.

3 istries, new structure determination methodologies, and integrative use of multiple experimental methods. RESULTS AND DISCUSSION The OneDep system ( provides a common portal for deposition of atomic coordinates and associated experimental data and metadata derived from the three currently supported methods of structure determination. Entries are processed using a standardized set of biocuration tools, with streamlining and automation of routine tasks. OneDep represents all incoming data in PDB exchange format (PDBx/mmCIF, mmcif.wwpdb.org) (Fitzgerald et al., 2005; Westbrook and Fitzgerald, 2009). Biocuration activities are distributed among the wwpdb partner sites, based on the geographic location from which the deposition originated. The OneDep system greatly simplifies data exchange and archival updating operations, and allows for remediation of the archive with reliable version control (Figure 2). The OneDep system was launched by the wwpdb partnership in January 2014, initially for atomic-level 3D structures determined by X-ray crystallography. In January 2016, in collaboration with EMDataBank (Lawson et al., 2016), the wwpdb developed and launched an extended version of OneDep that supports structures determined by X-ray crystallography, NMR, and 3DEM. The extended system interoperates with the repositories for NMR and 3DEM experimental data and assigns PDB codes and, when appropriate, BMRB and EMDB accession codes. The system replaces all legacy deposition/annotation systems previously in use by wwpdb partners, providing improved consistency and increased efficiency. Integrated Deposition User Interface The deposition module of the OneDep system was designed to meet the following objectives: Figure 1. Growth of the PDB Archive: Number of Entries Deposited Per Year; Number of Ligands Released Per Year; and Statistics on the Deposition of Large Structures existing deposition/biocuration tools and infrastructure. The wwpdb partners have, therefore, collaboratively developed a new unified system for data deposition, biocuration, and validation. The new system, OneDep, has been designed to meet evolving needs over the coming decades, including support for increasingly large systems, complex polymer and ligand chem- d Support for all major experimental techniques of macromolecular structure determination at atomic or nearatomic resolution (i.e., X-ray and neutron crystallography, NMR, and 3DEM), and any combination of these techniques. d Extensibility to permit inclusion of new data items for currently accepted (or new) structure determination methods. d Prevention of incomplete depositions. d Automated consistency checking during deposition. d Provision of preliminary validation reports for depositor review before deposition. d Distribution of deposition/biocuration/validation responsibilities among wwpdb Regional Data Centers. d Support for identical interfaces and equivalent levels of service to depositors located anywhere on the globe. To ensure the best possible support for PDB archival deposition/biocuration/validation, PDB depositors are directed to one of three wwpdb Regional Data Centers, on the basis of the location of the Principal Investigator s home institution: Europe and Africa / PDBe/UK; Asia and the Middle East / PDBj/Japan; and the Americas and Oceania / RCSB PDB/US. This new Structure 25, , March 7,

4 Deposition DEPOSITORS WORLDWIDE Harvest, Prepare, Pre-validate Data wwpdb OnePep UI NMR Files without coordinates BMRB Figure 2. Overview of the OneDep System: from Deposition, to Validation, to Biocuration, to Data Integration, and to Dissemination in Public Archives Biocuration Integration Dissemination Chemical Component Processing Map entries Master EMDB FTP Archive ** EMData Bank.org Master PDB FTP Archive * Public wwpdb FTP Archive Data Curation Sequence Processing RCSB PDB rcsb.org PDB FTP Archive Mirrors PDBe pdbe.org arrangement helps to ensure faster response times for communications and balanced distribution of the data curation and management load among wwpdb partners (Figure 3). Depositions of either experimental NMR data associated with structures that fall outside of the capabilities of the OneDep system or experimental NMR data not associated with the generation of a structure per se, are handled directly by the BMRB and PDBj-BMRB partner deposition sites. Once a depositor is transferred to the appropriate wwpdb deposition site, the depositor first registers a login session and then logs into the session to specify the experimental technique(s) used to determine the structure. This step enables OneDep to generate the appropriate categories for file upload and metadata input. Table 1 lists, for each type of deposition, the database accession codes that the system will issue and the mandatory and optional files for depositor upload. All uploaded files are checked for format compliance and data consistency. Atomic coordinates from all experimental methods and experimental data files from crystallography are converted into PDBx/mmCIF format, if 538 Structure 25, , March 7, 2017 Manual & Automated Annotation Validation PDBj pdbj.org Depositor review & approval Release processing NMR data BMRB bmrb. wisc.edu USERS WORLDWIDE * Maintained by RCSB PDB ** Maintained by PDBe necessary. The NMR chemical shifts are merged into a single NMR-STAR formatted file, and atom nomenclature correspondence between the chemical shift and atomic model files is verified. 3DEM volume maps are converted to a standard CCP4 format. If any of these steps fails, the depositor is asked to correct errors and re-upload data files. If format conversion and consistency checking are successful, a preliminary wwpdb validation report is generated. For depositor convenience, OneDep deposition pages can be pre-populated with metadata extracted directly from an uploaded PDBx/mmCIF file. Depositors are therefore encouraged to upload their data in PDBx/mmCIF format, as this approach permits richer and more complete capture of metadata, reducing the time required to complete the process and improving the quality of data in the PDB archive. Popular structure refinement packages already export PDBx/mmCIF formatted files, and the pdb_extract tool (Yang et al., 2004), can be used to prepare valid PDBx/mmCIF formatted files from legacy PDB format files and from output log files produced by most other software tools. The depositor then proceeds to enter mandatory information via the OneDep forms, which are broadly grouped into six categories: 1. Administrative information (e.g., author release instructions). 2. Description of each distinct macromolecule present in the sample. 3. Description of the experimental setup (e.g., sample preparation and data collection). 4. Description of experimental data, refinement (e.g., crystallographic refinement statistics), and software used. 5. Description and matching of ligands and modified polymer residues to the PDB Chemical Component Dictionary (CCD) (wwpdb.org/data/ccd; Westbrook et al., 2015). 6. Information on the quaternary structure and, whenever possible, experimental support for the biologically relevant assembly. Once all information has been harvested or entered via the OneDep forms, the depositor is required to review and accept

5 Figure 3. Workload Distribution To provide better support worldwide, new deposition sessions are directed to the wwpdb Regional Data Centers designated for processing based on geographic location: Europe and Africa / PDBe/UK; Asia and the Middle East / PDBj/Japan; and Americas and Oceania / RCSB PDB/US. the preliminary wwpdb validation report and to accept various repository terms and conditions in order to submit the deposition to the selected archive(s). Relevant accession codes are issued upon depositor acceptance. NMR spectroscopists are given the opportunity to upload additional NMR data, such as free induction decay, coupling constants, etc., at the ADIT-NMR portals hosted at BMRB and PDBj-BMRB. Depositors are strongly encouraged to pre-validate their experimental data/atomic coordinates by using the stand-alone wwpdb Validation Server (validate.wwpdb.org) and to correct any errors before initiating OneDep submission. During submission, the OneDep system allows replacement of atomic coordinates and/or experimental data should additional issues be detected. Structure Validation As the PDB archive grew and evolved (Figure 1), it became clear to the structural biology community that both structures and experimental data should be deposited and made publicly available (Berman et al., 2014). For X-ray and neutron crystallography, deposition of structure factors has been mandatory since For NMR structures, deposition of restraints has been mandatory since 2008, and assigned chemical shift deposition has been mandatory since As of September 2016, atomistic 3DEM structures deposited to the PDB must be accompanied by experimental mass density maps submitted to EMDB. Mandatory submission of experimental data opened the way for more extensive and meaningful validation of PDB structures. The wwpdb partners and EMDataBank have convened expert task forces in the fields of X-ray crystallography (Read et al., 2011), NMR (Montelione et al., 2013), and 3DEM (Henderson et al., 2012) to advise on suitable criteria, metrics, and software for validation of structures and associated experimental data. Most of these recommendations have been incorporated into a software pipeline that produces wwpdb validation reports in both human-readable (PDF) and machine-readable (XML) formats for all three currently supported experimental techniques. Reports for X-ray structures have been provided to depositors since August 2013 (Gore et al., 2012). Following further improvements, the final wwpdb validation reports for all publicly released X-ray entries were added to the PDB ftp archive and made available by the wwpdb partners in March In March 2016, wwpdb validation reports for all X-ray entries were refreshed with updated PDB archive statistics (computed at the end of calendar year 2015). wwpdb validation reports for NMR and 3DEM structures (also computed with end of 2015 statistics) were incorporated into the OneDep system and first provided to depositors in January Reports for all X-ray, NMR, and 3DEM entries in the PDB archive were made publicly available in May wwpdb validation reports are generated at four different stages: 1. Before deposition. The anonymous stand-alone wwpdb Validation Server ( can be used throughout structure determination/refinement. 2. During deposition. A preliminary version of the wwpdb validation report is provided to help identify issues with the atomic coordinates and/or data upload. The OneDep system supports revisions and upload of replacement files to finalize a submission. Once the preliminary wwpdb validation report is approved by the depositor, a PDB code is provided, and the submission is passed to a wwpdb biocurator for annotation and further consistency/error checking. Structure 25, , March 7,

6 Table 1. Structure depositions supported by OneDep: database accession codes issued by the system are identified with mandatory and optional file uploads Deposition type X-ray and neutron crystallography Database accession codes issued Mandatory file uploads Optional file uploads PDB Atomic coordinates Structure factor data Unmerged intensity data Solution and solid-state NMR PDB BMRB Atomic coordinates Assigned chemical shifts Restraints used in refinement Auxiliary sequence file from AMBER Electron crystallography PDB EMDB Atomic coordinates Structure factor data or Mass density map volume 3DEM (map and model) PDB EMDB Atomic coordinates Mass density map volume Entry image for public display (EMDB) 3DEM (map only) EMDB Mass density map volume Entry image for public display Ligand definition file or image Auxiliary files Spectral peak lists Ligand definition file or image Auxiliary files Ligand definition file or image Auxiliary files Any number of additional maps Any number of masks Two half maps Fourier shell correlation (FSC) curve Ligand definition file or image As above 3. Following deposition/annotation. This is the official wwpdb validation report, and depositors are strongly urged to submit these to journals with their manuscripts as supplementary material. 4. Upon release. The wwpdb validation report is re-generated and made public at the time of entry release. Validation reports produced at stages 1 and 2 should be considered preliminary, because they are based on uploaded data that may not fully comply with PDB archival standards. In addition, these reports provide only limited evaluation of ligands and any non-standard polymer residues. Validation reports produced at stages 3 and 4 include full analyses of ligand and polymer residues, and differ only in formatting details. The wwpdb has been working with journals and strongly encourages use of the final wwpdb validation report produced at stage 3 during manuscript review ( org/documentation/journals). As a result, many journals ( wwpdb.org/validation/validation-reports) now require wwpdb validation reports, for example, Structure ( com/blog/show-us-your-pdb-validation-reports) and Nature (Editorial, 2016). The wwpdb validation process involves three major assessment processes, which are summarized below. Knowledge-Based Validation of Atomic Coordinates Analyses include criteria such as too-close contacts between atoms, Ramachandran (F,J) polypeptide chain backbone torsion angle outlier statistics, rotameric states of protein side chains, pucker states of RNA ribose rings, etc., evaluated by the MolProbity software package (Chen et al., 2010). The geometry of small-molecule ligands is assessed by comparing them with related small-molecule crystal structures found in the Cambridge Structural Database (ccdc.cam.ac.uk/ solutions/csd-system/components/csd/) with the Mogul program (Bruno et al., 2004). For each evaluation criterion, a list of outliers is produced and an overall score is computed. For NMR structures, well-defined regions of proteins are identified by the Cyrange package, and the ill-defined regions are excluded from overall scoring (Kirchner and G untert, 2011; Montelione et al., 2013). Analysis of Experimental Data without Reference to Atomic Coordinates For X-ray entries, Phenix Xtriage (Adams et al., 2010) is used to analyze structure factor data, identify outliers, and detect the presence of crystal twinning, the presence of powder diffraction rings from ice, and other issues that may require the depositor s attention. For NMR entries, validation is currently limited to analyses of assigned chemical shifts highlighting referencing issues, completeness of resonance assignments, and statistically unusual chemical shifts. A prediction of protein disorder derived from the chemical shift data (random coil index) is also provided (Berjanskii and Wishart, 2005). For structures from 3DEM, limited information pertaining to the associated mass density map is provided. Assessment of the Fit between Atomic Coordinates and Experimental Data At present, these analyses are limited to crystal structures. The DCC program (Yang et al., 2016) is used to assess whether or not depositor-reported values for R factor and R-free can be reproduced. This check is normally performed by using the same refinement program as that specified by the depositor. In addition, the fit between the atomic coordinates and the experimental data is assessed by employing the EDS program MAPMAN (Kleywegt and Jones, 1996; Kleywegt et al., 2004), which uses REFMAC-calculated (Murshudov et al., 1997) electron density maps to compute the real space fit between atomic model coordinates and experimental electron density (real space R factor and correlation coefficient; RSR, RSCC) (Jones et al., 1991). The RSR score is normalized for each protein and nucleic acid residue type to obtain the RSR Z score (RSRZ) through comparison with other occurrences of the residue in PDB archive structures at similar diffraction data resolution. RSR and RSR Z scores are also used to assess the fit between the ligand atomic coordinates and the electron density map. An additional ligand-assessment parameter, local ligand density fit (LLDF), is used to compare the ligand RSR with that of its neighboring polymeric residues, taking crystallographic symmetry into account, in the form of a Z score. The official wwpdb validation report provides comprehensive details of the overall fit and flags outlier residues and outlier ligands with poor fit. 540 Structure 25, , March 7, 2017

7 Figure 4. Overview of the Biocuration Process Biocuration Pipeline The OneDep system uses a workflow management system to drive and monitor annotation, enabling consistent, efficient processing of multiple depositions in parallel. This workflow was designed to ensure completeness of annotation and to automate any necessary calculations, while providing interactive interfaces wherein the wwpdb biocurator can inspect interim and final results. Biocuration of a new deposition involves a variety of tasks, each of which typically involves bulk calculations followed by manual inspection/data input by an expert wwpdb biocurator (Figure 4). Each major task is carried out using a self-contained module. The Sequence Module (Figure 5) performs a BLAST (Altschul et al., 1990) search of the depositor-provided polymer sequences versus sequences from UniProt (UniProt Consortium, 2015) or NCBI GenBank (Benson et al., 2015). Multiple sequence alignments and 3D structure views are then displayed in this interface, allowing the biocurator to select the sequence reference that matches the organism and protein name provided by the depositor, and to annotate any sequence discrepancies. The Ligand Module (Figure 6) performs a batch sub-graph isomorphism search for deposited ligands and nonstandard polymer residues against the PDB CCD (Westbrook et al., 2015), and lists any matching chemical components, with interactive 2D and 3D ligand views that allow comparison between depositor-provided chemical information and the matched CCD entry. The biocurator can then accept the matched CCD entry, or launch a ligand editor to define a new chemical component when no appropriate CCD match is found (Sen et al., 2014; Young et al., 2013). Additional modules permit representation changes between polymeric and non-polymeric forms for peptide-like inhibitors/antibiotics (Dutta et al., 2014), value-added annotation such as secondary structure or connectivity between a ligand and neighboring polymer residues, method-specific annotation, etc. The Validation Module performs format and data consistency checks and generates the official wwpdb validation report. For X-ray crystallographic structures that contain ligands, the Validation Module assesses the fit of ligand atomic structure to the local ligand density (Figure 6). Once annotation is complete, the final model, experimental data, and validation files, as well as a summary report, are made available at the OneDep Deposition User Interface, and the depositor is invited by to log back into the session and review the curated data files and the official wwpdb validation report. Depositors and biocurators communicate with one another through a web-based interface integrated into the OneDep system, with alerts for pending messages. Depositors may provide corrections either by uploading new atomic coordinates and/or experimental data files, by making minor metadata corrections within the OneDep deposition pages, or by requesting through the communication interface that corrections be made by the biocurator. Upon receipt of such requests, the biocurator makes the depositor-requested changes. Following depositor approval, the newly completed PDB entry is made public according to the depositor s release instructions (wwpdb.org/documentation/ policy, N.B., the approved entry is released when wwpdb becomes aware that a manuscript associated with the PDB entry has been published). Infrastructure Design The OneDep system was developed using traditional multi-tier software architecture. A middleware layer consisting of the Python Django Framework ( is used to generate the HTML markup for the web-based deposition services. Access to data and computational tools is provided through a collection of Python application program interfaces (APIs) shared by all OneDep system components. These APIs provide uniform access to a variety of required tools (e.g., native Python tools, internal tools, libraries developed in C++, and community supported tools and libraries). To standardize and track the work of the wwpdb biocurators, the OneDep system uses a formal workflow specification system. These biocuration workflows are represented in a simple project-specific workflow definition language. Each workflow definition describes an ordered set of tasks together with the required inputs and expected outputs for each task. Workflow tasks map directly to our Python API entry points. A workflow daemon process monitors input workflow requests, manages the execution of workflow tasks, and records the completion status for each workflow task. The pool of workflow execution engines can be adjusted according to the computational demands of the biocuration workload. The OneDep biocurator web-based user interface provides access to the workflow and interactive biocuration tools. These tools are implemented as a modular collection of web services which wrap the functionality of our Python API. While each OneDep instance provides a complete set of deposition and biocuration functions, all wwpdb deposition sites exchange status and tracking information on an hourly schedule, and exchange data files on a daily basis, as part Structure 25, , March 7,

8 Figure 5. Sequence Annotation with the OneDep Depositor-provided polymer sequences are checked against atomic coordinate sequences and cross-referenced with UniProt/GenBank. of the coordinated weekly release of new and updated data into the PDB archive. Routine data exchange is currently supported by bidirectional RSYNC ( services among each OneDep instance. OneDep software updates, such as routine bug fixes, are tested, staged, and released on a biweekly maintenance schedule. The addition of substantial software features follows the same testing protocol, and occurs in combination with regular maintenance updates. The OneDep system allows deposition sessions to be exchanged between wwpdb Regional Data Centers. Should any OneDep site become unavailable, services can be redirected to a partner site to ensure continuity of service. When service at the former wwpdb site is resumed, the deposition sessions can be returned to it. This redirection and failover capability ensures that depositors worldwide will always be able to make a deposition and receive a PDB code, as required by most scientific journals. The wwpdb partners participate in supporting the full life cycle of the OneDep system. Software issues arising during system use are managed in a central JIRA tracking system ( and all wwpdb partners participate in reporting, troubleshooting, and resolving software issues. The global wwpdb software engineering team similarly continues to collaborate on defining requirements and designing, developing, testing, and deploying new and improved system features. These ongoing software development efforts are focused on delivering consistent, high-quality, and highly available PDB data to the structural biology community. Conclusion Since deployment of the OneDep system in January 2014, >21,000 structures have been deposited and annotated with it, and >15,000 of these structures have been publicly released. Based on 2 years of hands-on experience, the OneDep 542 Structure 25, , March 7, 2017

9 Figure 6. Ligand Annotation with the OneDep Depositor-provided chemical information for ligands is searched against the Chemical Component Dictionary (CCD) to identify and assign matching ligands. The interface (A) provides a list of matched chemical components and (B) captures and displays 2D and 3D views of the ligand from depositor-provided chemical information and the closest CCD match for review and assignment of the ligand ID. (C) A display of fit of the local electron density from the X-ray structure to the ligand allows rapid visual inspection. Deposition User Interface has been judged to be easier to use than legacy PDB deposition systems. For example, most (77%) depositions are completed within 48 hr from start to finish. Enhanced validation assists our depositors in improving the quality of their structures and the resulting PDB entries. Reliance on a modularized workflow has also yielded increased efficiencies in data processing. wwpdb biocurators report that automated processing of sequences and ligands has made it easier to process incoming structural data. The OneDep biocuration pipeline allows biocurators to perform multiple workflow tasks in parallel and to stop/start work on entries with minimal overhead and no loss of information. The OneDep system supports detailed tracking of every incoming PDB deposition, which enables performance assessments that could not be carried out with legacy PDB deposition systems. To measure system performance, we calculated the entry processing time, defined as the time taken between the annotation launch (Figure 4, step 1) and transmission of the biocuration report for depositor review/approval (Figure 4, step 7). Figure 7 shows three distinct peaks in the histogram Structure 25, , March 7,

10 AUTHOR CONTRIBUTIONS Major contributors for this project are: J.Y.Y., J.D.W., Z.F., R.S., E.P., T.J.O., S.S., and A.G. Deposition pipeline was developed by J.M.B., Z.F., A.G., P.M.H., L.M., M.S.M., T.J.O., E.S.G., and G.vG. Validation package was developed by Z.F., A.G., S.G., P.M.H., E.S.G., and H.Y. Biocuration pipeline was developed by L.C., D.D., Z.F., V.G., E.P., R.S., J.D.W., and H.Y. Workflow engine and infrastructure design was done by T.J.O., L.R., and J.D.W. Functional requirements were set by D.R.A., J.M.B., M.C., B.P.H., R.I., Y.I., N.K., C.L.L., S.M., A.M., A.P., E.P., I.P., S.S., M.R.S., C.S., G.J.S., E.L.U., R.Y., J.Y.Y., and M.A.Z. Weekly system unit testing was performed by D.R.A., J.M.B., B.P.H., Y.H.L., A.M., E.P., M.R.S., C.S., E.L.U., and J.Y.Y. Pre-production testing for each release was performed by J.M.B., M.C., L.D., S.G., B.P.H., R.I., Y.H.L., E.P., I.P., S.S., M.R.S., C.S., L.T., and M.A.Z. Overall project direction was provided by H.M.B., S.K.B., G.J.K., J.L.M., H.N., M.Q., S.V., and J.Y.Y. The manuscript was written by A.G., C.L.L., E.P., J.D.W., and J.Y.Y. ACKNOWLEDGMENTS Figure 7. Processing Time Per Entry for Steps 1 7 from Figure 4, Calculated for 18,300 Entries Received between January 2015 and June 2016 See main text for discussion of the three local maxima labeled (a) (c) in the distribution. of data processing time/entry in the OneDep system between January 2015 and June Peak (a) entry processing time (Figure 4, steps1/7) is less than 1 hr for the simplest cases that present no issues requiring manual intervention. Peak (b), for more complex entries requiring no manual intervention, entry processing time is 4 hr. Peak (c) for more challenging entries, 15 hr is required on average, because the depositor and biocurator need to confer during data processing. One percent of the entries in peak (c) took up to 20 days to resolve issues and complete data processing. This assessment has informed us that there is a need to shift peak (c) to peak (b) by promoting pre-deposition validation using a stand-alone wwpdb Validation Server. wwpdb biocurators report that efficiency increases result primarily from OneDep support for the automated processing of polymer sequences and ligands. Depositors upload atomic coordinate file replacements for about one-quarter of the entries (2,675/10,961 entries). For these 2,675 entries, a total of 3,530 atomic coordinate replacements have been received (average of 1.3 replacements/entry for those having at least one replacement upload). It appears, therefore, that depositors are responding to issues flagged in the wwpdb validation report by providing data of improved quality. This finding also points the way to further improvements to be made in preparing wwpdb validation reports and in streamlining the use of the stand-alone wwpdb Validation Server. Future enhancements to the wwpdb validation system will also focus on improved ligand validation as recommended by the recently conducted wwpdb/ccdc/d3r Ligand Validation Workshop (Adams et al., 2016). The authors thank all the members of worldwide PDB for their support and feedback, especially Kumaran Baskaran, Toshimichi Fujiwara, Takeshi Iwata, Yumiko Kengaku, Dimitri Maziuk, Manuel Fernandez Montecelo, Atsushi Nakagawa, Gaurav Sahni, Junko Sato, Raship Shah, Oliver S. Smart, Hirofumi Suzuki, Maria Voigt, and Hongyang Yao. RCSB PDB is supported by NSF (DBI ), NIH, DOE; PDBe by EMBL-EBI, Wellcome Trust (75968, 88944, ), BBSRC (BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/ M020428/1), EU (284209, ) and MRC (MR/L007835/1); PDBj and PDBj-BMRB by JST-NBDC, BMRB by NIGMS (GM109046); and EMDataBank partners at PDBe and RCSB PDB by NIGMS (GM079429). Received: September 30, 2016 Revised: November 8, 2016 Accepted: January 10, 2017 Published: February 9, 2017 REFERENCES Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, Adams, P.D., Aertgeerts, K., Bauer, C., Bell, J.A., Berman, H.M., Bhat, T.N., Blaney, J.M., Bolton, E., Bricogne, G., Brown, D., et al. (2016). Outcome of the first wwpdb/ccdc/d3r ligand validation workshop. Structure 24, Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, Benson, D.A., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. (2015). GenBank. Nucleic Acids Res. 43, D30 D35. Berjanskii, M.V., and Wishart, D.S. (2005). A simple method to predict protein flexibility using secondary chemical shifts. J. Am. Chem. Soc. 127, Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000). The protein data bank. Nucleic Acids Res. 28, Berman, H., Henrick, K., and Nakamura, H. (2003). Announcing the worldwide protein data bank. Nat. Struct. Biol. 10, 980. Berman, H.M., Kleywegt, G.J., Nakamura, H., and Markley, J.L. (2013). The future of the protein data bank. Biopolymers 99, Berman, H.M., Kleywegt, G.J., Nakamura, H., and Markley, J.L. (2014). The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. 28, Bruno, I.J., Cole, J.C., Kessler, M., Luo, J., Motherwell, W.D., Purkis, L.H., Smith, B.R., Taylor, R., Cooper, R.I., Harris, S.E., and Orpen, A.G. (2004). 544 Structure 25, , March 7, 2017

11 Retrieval of crystallographically-derived molecular geometry information. J. Chem. Inf. Comput. Sci. 44, Chen, V.B., Arendall, W.B., 3rd, Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., and Richardson, D.C. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, Dutta, S., Dimitropoulos, D., Feng, Z., Persikova, I., Sen, S., Shao, C., Westbrook, J., Young, J., Zhuravleva, M.A., Kleywegt, G.J., and Berman, H.M. (2014). Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers 101, Editorial. (2016). Where are the data? Nat. Struct. Mol. Biol. 23, 871. Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P.E., McMahon, B., Watenpaugh, K.D., and Berman, H.M. (2005). 4.5 Macromolecular dictionary (mmcif). In International Tables for Crystallography G. Definition and Exchange of Crystallographic Data, S.R. Hall and B. McMahon, eds. (Springer), pp Gore, S., Velankar, S., and Kleywegt, G.J. (2012). Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr. 68, Henderson, R., Sali, A., Baker, M.L., Carragher, B., Devkota, B., Downing, K.H., Egelman, E.H., Feng, Z., Frank, J., Grigorieff, N., et al. (2012). Outcome of the first electron microscopy validation task force meeting. Structure 20, Jones, T.A., Zou, J.-Y., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47, Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A., and Nakamura, H. (2012). Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 40, D453 D460. Kirchner, D.K., and G untert, P. (2011). Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12, 170. Kleywegt, G.J., and Jones, T.A. (1996). xdlmapman and xdldataman - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr. 52, Kleywegt, G.J., Harris, M.R., Zou, J.Y., Taylor, T.C., Wahlby, A., and Jones, T.A. (2004). The Uppsala electron-density server. Acta Crystallogr. D Biol. Crystallogr. 60, Lawson, C.L., Patwardhan, A., Baker, M.L., Hryc, C., Garcia, E.S., Hudson, B.P., Lagerstedt, I., Ludtke, S.J., Pintilie, G., Sala, R., et al. (2016). EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 44, D396 D403. Montelione, G.T., Nilges, M., Bax, A., Guntert, P., Herrmann, T., Richardson, J.S., Schwieters, C.D., Vranken, W.F., Vuister, G.W., Wishart, D.S., et al. (2013). Recommendations of the wwpdb NMR validation task force. Structure 21, Murshudov, G.N., Vagin, A.A., and Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, Protein Data Bank. (1971). Protein data bank. Nat. New Biol. 233, 223. Read, R.J., Adams, P.D., Arendall, W.B., 3rd, Brunger, A.T., Emsley, P., Joosten, R.P., Kleywegt, G.J., Krissinel, E.B., Lutteke, T., Otwinowski, Z., et al. (2011). A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19, Sen, S., Young, J., Berrisford, J.M., Chen, M., Conroy, M.J., Dutta, S., Di Costanzo, L., Gao, G., Ghosh, S., Hudson, B.P., et al. (2014). Small molecule annotation for the protein data bank. Database (Oxford) 2014, bau116. Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., et al. (2008). BioMagResBank. Nucleic Acids Res. 36, D402 D408. UniProt Consortium (2015). UniProt: a hub for protein information. Nucleic Acids Res. 43, D204 D212. Velankar, S., van Ginkel, G., Alhroub, Y., Battle, G.M., Berrisford, J.M., Conroy, M.J., Dana, J.M., Gore, S.P., Gutmanas, A., Haslam, P., et al. (2016). PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res. 44, D385 D395. Westbrook, J.D., and Fitzgerald, P.M.D. (2009). Chapter 10 the PDB format, mmcif formats, and other data formats. In Structural Bioinformatics, Second Edition, P.E. Bourne and J. Gu, eds. (John Wiley & Sons, Inc), pp Westbrook, J.D., Shao, C., Feng, Z., Zhuravleva, M., Velankar, S., and Young, J. (2015). The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinformatics 31, Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H.M., and Westbrook, J.D. (2004). Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr. 60, Yang, H., Peisach, E., Westbrook, J.D., Young, J., Berman, H.M., and Burley, S.K. (2016). DCC: a Swiss army knife for structure factor analysis and validation. J. Appl. Crystallogr. 49, Young, J.Y., Feng, Z., Dimitropoulos, D., Sala, R., Westbrook, J., Zhuravleva, M., Shao, C., Quesada, M., Peisach, E., and Berman, H.M. (2013). Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database (Oxford) 2013, bat079. Structure 25, , March 7,