RCSB Protein Data Bank 1D Tools and Services

Motivation

Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function.

Results

Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web.

Availabilityand implementation

https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro.

Supplementary information

Supplementary data are available at Bioinformatics online.

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’

The TRUST Principles for digital repositories

As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold.

Archiving and disseminating integrative structure models

Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Protein Data Bank: the single global archive for 3D macromolecular structure data

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.

Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton-feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt-cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD-seq-enabled genome scan to identify loci with significant allele frequency changes over the 15-year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

A systems science perspective on the capacity for change in public hospitals

Many types of organisation are difficult to change, mainly due to structural, cultural and contextual barriers. Change in public hospitals is arguably even more problematic than in other types of hospitals, due to features such as structural dysfunctionalities and bureaucracy stemming from being publicly-run institutions. The main goals of this commentary are to bring into focus and highlight the "3 + 3 Decision Framework" proposed by Edwards and Saltman. This aims to help guide policymakers and managers implementing productive change in public hospitals. However, while change from the top is popular, there are powerful front-line clinicians, especially doctors, who can act to counterbalance top-down efforts. Front-line clinicians have cultural characteristics and power that allows them to influence or reject managerial decisions. Clinicians in various lower-level roles can also influence other clinicians to resist or ignore management requirements. The context is further complicated by multi-stakeholder agendas, differing goals, and accumulated inertia. The special status of clinicians, along with other system features of public hospitals, should be factored into efforts to realise major system improvements and progressive change.

The fern cavitation catapult: mechanism and design principles

Leptosporangiate ferns have evolved an ingenious cavitation catapult to disperse their spores. The mechanism relies almost entirely on the annulus, a row of 12-25 cells, which successively: (i) stores energy by evaporation of the cells' content, (ii) triggers the catapult by internal cavitation, and (iii) controls the time scales of energy release to ensure efficient spore ejection. The confluence of these three biomechanical functions within the confines of a single structure suggests a level of sophistication that goes beyond most man-made devices where specific structures or parts rarely serve more than one function. Here, we study in detail the three phases of spore ejection in the sporangia of the fern Polypodium aureum. For each of these phases, we have written the governing equations and measured the key parameters. For the opening of the sporangium, we show that the structural design of the annulus is particularly well suited to inducing bending deformations in response to osmotic volume changes. Moreover, the measured parameters for the osmoelastic design lead to a near-optimal speed of spore ejection (approx. 10 m s(-1)). Our analysis of the trigger mechanism by cavitation points to a critical cavitation pressure of approximately -100 ± 14 bar, a value that matches the most negative pressures recorded in the xylem of plants. Finally, using high-speed imaging, we elucidated the physics leading to the sharp separation of time scales (30 versus 5000 µs) in the closing dynamics. Our results highlight the importance of the precise tuning of the parameters without which the function of the leptosporangium as a catapult would be severely compromised.

Emotional Awareness Moderates the Relationship Between Childhood Abuse and Borderline Personality Disorder Symptom Factors

OBJECTIVE

To examine pathways to borderline personality disorder (BPD), focusing on childhood abuse and emotional attention and clarity.

METHOD

Among 293 community residents (mean age = 43.1; 53.9% female), measured associations between the BPD symptom factors of disturbed relatedness, affective dysregulation, and behavioral dysregulation and (a) childhood abuse (emotional, physical, and sexual); (b) emotional attention and clarity; and (c) negative affect, using structured interviews, the Schedule for Non-Adaptive and Adaptive Personality-2, the Trait Meta Mood Scale, and the Positive and Negative Affect Scale, respectively.

RESULTS

All forms of childhood abuse were associated with BPD symptom factors. Emotional attention and clarity moderated the effects of childhood physical and emotional abuse on behavioral dysregulation and disturbed relatedness. All results held when controlling for negative affect.

CONCLUSION

The relations between childhood abuse and BPD are robust. Emotional attention and clarity may help elucidate the links between childhood abuse and BPD.

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014.

Extension of the sasCIF format and its applications for data processing and deposition

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. This update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.

Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium)

The report that the cotton leaf perforator, Bucculatrix thurberiella, is one of the few insect herbivores to attack Gossypium thurberi prompted an investigation of the terpenoids present in the leaves of this wild species of cotton. Members of Gossypium produce subepidermal pigment glands in their leaves that contain the dimeric sesquiterpenoid gossypol as well as other biosynthetically related terpenoids. In addition to gossypol, a previously unknown dimeric sesquiterpenoid, gossypolhemiquinone (GHQ), was identified in trace amounts in G. thurberi, a member of the D genome. Other members of the D genome of Gossypium were subsequently found to contain this compound, but GHQ was not detected in commercial cotton cultivars. When fed to Helicoverpa zea in an artificial diet, GHQ delayed days-to-pupation, reduced pupal weights, and survival to adulthood to a lesser or equal extent than gossypol in comparison to the control diet. However, GHQ had a synergistic effect on survival and days-to-pupation when combined with gossypol at the highest dosage tested (0.18%; 15.5:84.5 GHQ:gossypol). Because gossypol exhibits anti-cancer activity, GHQ was also evaluated for its anti-cancer activity against the National Cancer Institute's 60-Human Tumor Cell Line Screen. Significant inhibitory activity against most of these cell lines was not observed, but the results may offer some promise against leukemia cancer cell lines.

Vital signs monitoring and nurse-patient interaction: A qualitative observational study of hospital practice

BACKGROUND

High profile safety failures have demonstrated that recognising early warning signs of clinical and physiological deterioration can prevent or reduce harm resulting from serious adverse events. Early warning scoring systems are now routinely used in many places to detect and escalate deteriorating patients. Timely and accurate vital signs monitoring are critical for ensuring patient safety through providing data for early warning scoring systems, but little is known about current monitoring practices.

OBJECTIVE

To establish a profile of nurses' vital signs monitoring practices, related dialogue, and adherence to health service protocol in New South Wales, Australia.

METHODS

Direct observations of nurses' working practices were conducted in two wards. The observations focused on times of the day when vital signs were generally measured. Patient interactions were recorded if occurring any time during the observation periods. Participants (n=42) included nursing staff on one chronic disease medical and one acute surgical ward in a large urban teaching hospital in New South Wales.

RESULTS

We observed 441 patient interactions. Measurement of vital signs occurred in 52% of interactions. The minimum five vital signs measures required by New South Wales Health policy were taken in only 6-21% of instances of vital signs monitoring. Vital signs were documented immediately on 93% of vitals-taking occasions and documented according to the policy in the patient's chart on 89% of these occasions. Nurse-patient interactions were initiated for the purpose of taking vital signs in 49% of interactions, with nurse-patient discourse observed during 88% of all interactions. Nurse-patient dialogue led to additional care being provided to patients in 12% of interactions.

CONCLUSION

The selection of appropriate vital signs measured and responses to these appears to rely on nurses' clinical judgement or time availability rather than on policy-mandated frequency. The prevalence of incomplete sets of vital signs may limit identification of deteriorating patients. The findings from this study present an important baseline profile against which to evaluate the impact of introducing continuous monitoring approaches on current hospital practice.

The Impact of a Health IT Changeover on Medical Imaging Department Work Processes and Turnaround Times: A mixed method study

OBJECTIVES

To assess the impact of introducing a new Picture Archiving and Communication System (PACS) and Radiology Information System (RIS) on: (i) Medical Imaging work processes; and (ii) turnaround times (TATs) for x-ray and CT scan orders initiated in the Emergency Department (ED).

METHODS

We employed a mixed method study design comprising: (i) semi-structured interviews with Medical Imaging Department staff; and (ii) retrospectively extracted ED data before (March/April 2010) and after (March/April 2011 and 2012) the introduction of a new PACS/RIS. TATs were calculated as: processing TAT (median time from image ordering to examination) and reporting TAT (median time from examination to final report).

RESULTS

Reporting TAT for x-rays decreased significantly after introduction of the new PACS/RIS; from a median of 76 hours to 38 hours per order (p<.0001) for patients discharged from the ED, and from 84 hours to 35 hours (p<.0001) for patients admitted to hospital. Medical Imaging staff reported that the changeover to the new PACS/RIS led to gains in efficiency, particularly regarding the accessibility of images and patient-related information. Nevertheless, assimilation of the new PACS/RIS with existing Departmental work processes was considered inadequate and in some instances unsafe. Issues highlighted related to the synchronization of work tasks (e.g., porter arrangements) and the material set up of the work place (e.g., the number and location of computers).

CONCLUSIONS

The introduction of new health IT can be a "double-edged sword" providing improved efficiency but at the same time introducing potential hazards affecting the effectiveness of the Medical Imaging Department.

Data to knowledge: how to get meaning from your result

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Design challenges for electronic medication administration record systems in residential aged care facilities: a formative evaluation

INTRODUCTION

Electronic medication administration record (eMAR) systems are promoted as a potential intervention to enhance medication safety in residential aged care facilities (RACFs). The purpose of this study was to conduct an in-practice evaluation of an eMAR being piloted in one Australian RACF before its roll out, and to provide recommendations for system improvements.

METHODS

A multidisciplinary team conducted direct observations of workflow (n=34 hours) in the RACF site and the community pharmacy. Semi-structured interviews (n=5) with RACF staff and the community pharmacist were conducted to investigate their views of the eMAR system. Data were analysed using a grounded theory approach to identify challenges associated with the design of the eMAR system.

RESULTS

The current eMAR system does not offer an end-to-end solution for medication management. Many steps, including prescribing by doctors and communication with the community pharmacist, are still performed manually using paper charts and fax machines. Five major challenges associated with the design of eMAR system were identified: limited interactivity; inadequate flexibility; problems related to information layout and semantics; the lack of relevant decision support; and system maintenance issues. We suggest recommendations to improve the design of the eMAR system and to optimize existing workflows.

DISCUSSION

Immediate value can be achieved by improving the system interactivity, reducing inconsistencies in data entry design and offering dedicated organisational support to minimise connectivity issues. Longer-term benefits can be achieved by adding decision support features and establishing system interoperability requirements with stakeholder groups (e.g. community pharmacies) prior to system roll out. In-practice evaluations of technologies like eMAR system have great value in identifying design weaknesses which inhibit optimal system use.

The role of the nitric oxide pathway in brain injury and its treatment--from bench to bedside

Nitric oxide (NO) is a key signalling molecule in the regulation of cerebral blood flow. This review summarises current evidence regarding the role of NO in the regulation of cerebral blood flow at rest, under physiological conditions, and after brain injury, focusing on subarachnoid haemorrhage, traumatic brain injury, and ischaemic stroke and following cardiac arrest. We also review the role of NO in the response to hypoxic insult in the developing brain. NO depletion in ischaemic brain tissue plays a pivotal role in the development of subsequent morbidity and mortality through microcirculatory disturbance and disordered blood flow regulation. NO derived from endothelial nitric oxide synthase (eNOS) appears to have neuroprotective properties. However NO derived from inducible nitric oxide synthase (iNOS) may have neurotoxic effects. Cerebral NO donor agents, for example sodium nitrite, appear to replicate the effects of eNOS derived NO, and therefore have neuroprotective properties. This is true in both the adult and immature brain. We conclude that these agents should be further investigated as targeted pharmacotherapy to protect against secondary brain injury.

Structural Biology Knowledgebase: An Integrated Resource for Modern Biologists

"The Structural Biology Knowledgebase (SBKB, http://sbkb.org) was established as a data aggregator to facilitate research design and analysis for a wide variety of biological systems. It serves as a single resource that integrates structure, sequence, and functional annotations plus technical information regarding protein production and structure determination. Researchers can search the SBKB by sequence, PDB ID or UniProt accession code, and receive an up-to-the-minute list of matching 3D experimental structures from the Protein Data Bank, pre-built theoretical models from the Protein Model Portal, annotations from 100+ open biological resources, structural genomics target histories and protocols from TargetTrack, and ready-to-use DNA clones from DNASU. It also possible to find structures according to functional relevance (KB-Rank tool), or find related technologies and publications from the PSI Technology and Publications Portals, respectively. Interactive tools such as real-time theoretical modeling and biophysical parameter prediction also enhance understanding of proteins that are not yet well characterized. Experimentally-focused ""hubs"" collect links to helpful tools and resources for the areas of Structural Targets; Structure, Sequence and Function; Homology Models, Methods and Technologies, and Membrane Proteins. In partnership with the Nature Publishing Group, latest research highlights and articles on specific biological systems are written monthly to share the impact of structural biology. This presentation will demonstrate how the SBKB turns data into knowledge and enables further research. SBKB is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health (U01 GM093324)."

The New wwPDB Deposition and Annotation System

In anticipation of continued growth in the number, size and complexity of the structures that are being studied and deposited in the PDB and EMDB, the Worldwide Protein Data Bank (wwPDB) has developed a new system for deposition and annotation of structural data. The new wwPDB Deposition & Annotation (D&A) system offers a single entry point for depositors from around the world to deposit X-ray, NMR, 3DEM data, receive detailed validation feedback, and preview annotations, all prior to submission. The system will assign not only PDB identifiers upon submission, but also EMDB and BMRB identifiers for 3DEM and NMR data, respectively. Furthermore, the new system is used at all wwPDB processing sites around the globe. After deposition, wwPDB annotators use the system for sequence annotation, ligand annotation, additional structure analysis and validation, and review. Validation functionality implements recommendations from the wwPDB X-ray Validation Task Force and produces a structure validation report for depositor review and submission to scientific journals. Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) through the end of 2014. At that time, the legacy tools will stop accepting new entries, and will only be available for a limited period of time to complete in-progress deposition sessions. An important feature of the new deposition system is its ability to accept and produce data in PDBx/mmCIF format, which has no limitations in the size or complexity of structures that can be represented. The PDBx/mmCIF Working Group, consisting of software developers from CCP4, Global Phasing Ltd., Phenix, and the wwPDB, have adapted structure determination software packages to produce PDBx/mmCIF format files suitable for deposition. The new wwPDB deposition and annotation will produce more consistent and higher quality archive entries, and will improve the efficiency and throughput of deposition and annotation. The modular design of the system will facilitate incorporating new functionalities and support for hybrid and other methods in the future. wwPDB members are RCSB PDB (supported by NSF, NIH, and DOE), PDBe (EMBL-EBI, Wellcome Trust, BBSRC, NIGMS, and EU), PDBj (NBDC-JST) and BMRB (NLM).

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB

This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org.