PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

The structure assessment web server: for proteins, complexes and more

The 'structure assessment' web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.

Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure

In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble-function predictions, analogous to the achievements of AlphaFold with single-structure prediction.

Efficient protein structure archiving using ProteStAr

MOTIVATION

The introduction of Deep Minds' Alpha Fold 2 enabled the prediction of protein structures at an unprecedented scale. AlphaFold Protein Structure Database and ESM Metagenomic Atlas contain hundreds of millions of structures stored in CIF and/or PDB formats. When compressed with a general-purpose utility like gzip, this translates to tens of terabytes of data, which hinders the effective use of predicted structures in large-scale analyses.

RESULTS

Here, we present ProteStAr, a compressor dedicated to CIF/PDB, as well as supplementary PAE files. Its main contribution is a novel approach to predicting atom coordinates on the basis of the previously analyzed atoms. This allows efficient encoding of the coordinates, the largest component of the protein structure files. The compression is lossless by default, though the lossy mode with a controlled maximum error of coordinates reconstruction is also present. Compared to the competing packages, i.e. BinaryCIF, Foldcomp, PDC, our approach offers a superior compression ratio at established reconstruction accuracy. By the efficient use of threads at both compression and decompression stages, the algorithm takes advantage of the multicore architecture of current central processing units and operates with speeds of about 1 GB/s. The presence of Python and C++ API further increases the usability of the presented method.

AVAILABILITY AND IMPLEMENTATION

The source code of ProteStAr is available at https://github.com/refresh-bio/protestar.

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank

The Protein Data Bank (PDB) is the global repository for public-domain experimentally determined 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from trusted external biodata resources. While each Worldwide PDB (wwPDB) partner has made best efforts to provide up-to-date external annotations, accessing and integrating information from disparate wwPDB data centers can be an involved process. To address this issue, the wwPDB has established the PDB Next Generation (or NextGen) Archive, developed to centralize and streamline access to enriched structural annotations from wwPDB partners and trusted external sources. At present, the NextGen Archive provides mappings between experimentally determined 3D structures of proteins and UniProt amino acid sequences, domain annotations from Pfam, SCOP2 and CATH databases and intra-molecular connectivity information. Since launch, the PDB NextGen Archive has seen substantial user engagement with over 3.5 million data file downloads, ensuring researchers have access to accurate, up-to-date and easily accessible structural annotations. Database URL: http://www.wwpdb.org/ftp/pdb-nextgen-archive-site.

Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining

BACKGROUND

Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored.

RESULTS

Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome.

CONCLUSIONS

This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. Video Abstract.

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

gmXtal: Cooking Crystals with GROMACS

Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution, because this is their native environment. However, the structures used in such simulations are often obtained with X-ray crystallography, which provides the atomic coordinates of the biomolecule in a crystal environment. With the advent of free electron lasers and time-resolved techniques, X-ray crystallography can now also access metastable states that are intermediates in a biochemical process. Such experiments provide additional data, which can be used, for example, to optimize MD force fields. Doing so requires that the simulation of the biomolecule is also performed in the crystal environment. However, in contrast to simulations of biomolecules in solution, setting up a crystal is challenging. In particular, because not all solvent molecules are resolved in X-ray crystallography, adding a suitable number of solvent molecules, such that the properties of the crystallographic unit cell are preserved in the simulation, can be difficult and typically is a trial-and-error based procedure requiring manual interventions. Such interventions preclude high throughput applications. To overcome this bottleneck, we introduce gmXtal, a tool for setting up crystal simulations for MD simulations with GROMACS. With the information from the protein data bank (rcsb.org) gmXtal automatically (i) builds the crystallographic unit cell; (ii) sets the protonation of titratable residues; (iii) builds missing residues that were not resolved experimentally; and (iv) adds an appropriate number of solvent molecules to the system. gmXtal is available as a standalone tool https://gitlab.com/pbuslaev/gmxtal .

Structural highlights of macromolecular complexes and assemblies

The structures of macromolecular assemblies have given us deep insights into cellular processes and have profoundly impacted biological research and drug discovery. We highlight the structures of macromolecular assemblies that have been modeled using integrative and computational methods and describe how open access to these structures from structural archives has empowered the research community. The arsenal of experimental and computational methods for structure determination ensures a future where whole organelles and cells can be modeled.

RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction

With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA structure prediction has recently received increased attention from deep learning researchers. RNAs introduce substantial challenges due to the sparser availability and lower structural diversity of the experimentally resolved RNA structures in comparison to protein structures. These challenges are often poorly addressed by the existing literature, many of which report inflated performance due to using training and testing sets with significant structural overlap. Further, the most recent Critical Assessment of Structure Prediction (CASP15) has shown that deep learning models for RNA structure are currently outperformed by traditional methods. In this paper we present RNA3DB, a dataset of structured RNAs, derived from the Protein Data Bank (PDB), that is designed for training and benchmarking deep learning models. The RNA3DB method arranges the RNA 3D chains into distinct groups (Components) that are non-redundant both with regard to sequence as well as structure, providing a robust way of dividing training, validation, and testing sets. Any split of these structurally-dissimilar Components are guaranteed to produce test and validations sets that are distinct by sequence and structure from those in the training set. We provide the RNA3DB dataset, a particular train/test split of the RNA3DB Components (in an approximate 70/30 ratio) that will be updated periodically. We also provide the RNA3DB methodology along with the source-code, with the goal of creating a reproducible and customizable tool for producing structurally-dissimilar dataset splits for structural RNAs.

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.

RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction

With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA structure prediction has recently received increased attention from deep learning researchers. RNAs introduce substantial challenges due to the sparser availability and lower structural diversity of the experimentally resolved RNA structures in comparison to protein structures. These challenges are often poorly addressed by the existing literature, many of which report inflated performance due to using training and testing sets with significant structural overlap. Further, the most recent Critical Assessment of Structure Prediction (CASP15) has shown that deep learning models for RNA structure are currently outperformed by traditional methods. In this paper we present RNA3DB, a dataset of structured RNAs, derived from the Protein Data Bank (PDB), that is designed for training and benchmarking deep learning models. The RNA3DB method arranges the RNA 3D chains into distinct groups (Components) that are non-redundant both with regard to sequence as well as structure, providing a robust way of dividing training, validation, and testing sets. Any split of these structurally-dissimilar Components are guaranteed to produce test and validations sets that are distinct by sequence and structure from those in the training set. We provide the RNA3DB dataset, a particular train/test split of the RNA3DB Components (in an approximate 70/30 ratio) that will be updated periodically. We also provide the RNA3DB methodology along with the source-code, with the goal of creating a reproducible and customizable tool for producing structurally-dissimilar dataset splits for structural RNAs.

Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER

The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually archived along with the atomic coordinates. It is shown here that the availability of unmerged reflection data enables valuable additional analyses to be performed that yield improvements in the final models, and tools are presented to implement them, together with examples of the results to which they give access. The first example is the automatic identification and removal of image ranges affected by loss of crystal centering or by excessive decay of the diffraction pattern as a result of radiation damage. The second example is the `reflection-auditing' process, whereby individual merged data items showing especially poor agreement with model predictions during refinement are investigated thanks to the specific metadata (such as image number and detector position) that are available for the corresponding unmerged data, potentially revealing previously undiagnosed instrumental, experimental or processing problems. The third example is the calculation of so-called F(early) - F(late) maps from carefully selected subsets of unmerged amplitude data, which can not only highlight the location and extent of radiation damage but can also provide guidance towards suitable fine-grained parametrizations to model the localized effects of such damage.

Parameterization of General Organic Polymers within the Open Force Field Framework

Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.

3D animation as a tool for integrative modeling of dynamic molecular mechanisms

As the scientific community accumulates diverse data describing how molecular mechanisms occur, creating and sharing visual models that integrate the richness of this information has become increasingly important to help us explore, refine, and communicate our hypotheses. Three-dimensional (3D) animation is a powerful tool to capture dynamic hypotheses that are otherwise difficult or impossible to visualize using traditional 2D illustration techniques. This perspective discusses the current and future roles that 3D animation can play in the research sphere.

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information

The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of "recognition entropy", related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d.

EMDB-the Electron Microscopy Data Bank

The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells

SUMMARY

pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures.

AVAILABILITY AND IMPLEMENTATION

pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.

Discussion on structure classification and regulation function of histone deacetylase and their inhibitor

Epigenetic regulation of genes through posttranslational regulation of proteins is a well-explored approach for disease treatment, particularly in cancer chemotherapy. Histone deacetylases have shown significant potential as effective drug targets in therapeutic studies aiming to restore epigenetic normality in oncology. Besides their role in modifying histones, histone deacetylases can also catalyze the deacetylation of various nonhistone proteins and participate in the regulation of multiple biological processes. This paper provides a review of the classification, structure, and functional characteristics of the four classes of human histone deacetylases. The increasing abundance of structural information on HDACs has led to the gradual elucidation of structural differences among subgroups and subtypes. This has provided a reasonable explanation for the selectivity of certain HDAC inhibitors. Currently, the US FDA has approved a total of six HDAC inhibitors for marketing, primarily for the treatment of various hematological tumors and a few solid tumors. These inhibitors all have a common pharmacodynamic moiety consisting of three parts: CAP, ZBG, and Linker. In this paper, the structure-effect relationship of HDAC inhibitors is explored by classifying the six HDAC inhibitors into three main groups: isohydroxamic acids, benzamides, and cyclic peptides, based on the type of inhibitor ZBG. However, there are still many questions that need to be answered in this field. In this paper, the structure-functional characteristics of HDACs and the structural information of the pharmacophore model and enzyme active region of HDAC is are considered, which can help to understand the inhibition mechanism of the compounds as well as the rational design of HDACs. This paper integrates the structural-functional characteristics of HDACs as well as the pharmacophore model of HDAC is and the structural information of the enzymatic active region, which not only contributes to the understanding of the inhibition mechanism of the compounds, but also provides a basis for the rational design of HDAC inhibitors.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.

Standardizing macromolecular structure files: further efforts are needed

Investigating large datasets of biological information by automatic procedures may offer chances of progress in knowledge. Recently, tremendous improvements in structural biology have allowed the number of structures in the Protein Data Bank (PDB) archive to increase rapidly, in particular those for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated proteins. However, their automatic analysis can be hampered by the nonuniform descriptors used by authors in some records of the PDB and PDBx/mmCIF files. In this opinion article we highlight the difficulties encountered in automating the analysis of hundreds of structures, suggesting that further standardization of the description of these molecular entities and of their attributes, generalized to the macromolecular structures contained in the PDB, might generate files more suitable for automatized analyses of a large number of structures.

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data

More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.

RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. The RCSB PDB RCSB.org research-focused web portal is used annually by many millions of users around the world. They access biostructure information, run complex queries utilizing various search services (e.g., full-text, structural and chemical attribute, chemical, sequence, and structure similarity searches), and visualize macromolecules in 3D, all at no charge and with no limitations on data usage. Notwithstanding more than 24,000-fold growth of the PDB over the past five decades, experimentally-determined structures are only available for a small subset of the millions of proteins of known sequence. Recently developed machine learning software tools can predict 3D structures of proteins at accuracies comparable to lower-resolution experimental methods. The RCSB PDB now provides access to ∼1,000,000 Computed Structure Models (CSMs) of proteins coming from AlphaFold DB and the ModelArchive alongside ∼200,000 experimentally-determined PDB structures. Both CSMs and PDB structures are available on RCSB.org and via well-established RCSB PDB Data, Search, and 1D-Coordinates application programming interfaces (APIs). Simultaneous delivery of PDB data and CSMs provides users with access to complementary structural information across the human proteome and those of model organisms and selected pathogens. API enhancements are backwards-compatible and programmatic users can "opt in" to access CSMs with minimal effort. Herein, we describe modifications to RCSB PDB cyberinfrastructure required to support sixfold scaling of 3D biostructure data delivery and lay the groundwork for scaling to accommodate hundreds of millions of CSMs.

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

AlphaFill: enriching AlphaFold models with ligands and cofactors

Artificial intelligence-based protein structure prediction approaches have had a transformative effect on biomolecular sciences. The predicted protein models in the AlphaFold protein structure database, however, all lack coordinates for small molecules, essential for molecular structure or function: hemoglobin lacks bound heme; zinc-finger motifs lack zinc ions essential for structural integrity and metalloproteases lack metal ions needed for catalysis. Ligands important for biological function are absent too; no ADP or ATP is bound to any of the ATPases or kinases. Here we present AlphaFill, an algorithm that uses sequence and structure similarity to 'transplant' such 'missing' small molecules and ions from experimentally determined structures to predicted protein models. The algorithm was successfully validated against experimental structures. A total of 12,029,789 transplants were performed on 995,411 AlphaFold models and are available together with associated validation metrics in the alphafill.eu databank, a resource to help scientists make new hypotheses and design targeted experiments.

The curse of the protein ribbon diagram

Does reductionism, in the era of machine learning and now interpretable AI, facilitate or hinder scientific insight? The protein ribbon diagram, as a means of visual reductionism, is a case in point.

Biological Magnetic Resonance Data Bank

The Biological Magnetic Resonance Data Bank (BMRB, https://bmrb.io) is the international open data repository for biomolecular nuclear magnetic resonance (NMR) data. Comprised of both empirical and derived data, BMRB has applications in the study of biomacromolecular structure and dynamics, biomolecular interactions, drug discovery, intrinsically disordered proteins, natural products, biomarkers, and metabolomics. Advances including GHz-class NMR instruments, national and trans-national NMR cyberinfrastructure, hybrid structural biology methods and machine learning are driving increases in the amount, type, and applications of NMR data in the biosciences. BMRB is a Core Archive and member of the World-wide Protein Data Bank (wwPDB).

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.

A roadmap for the functional annotation of protein families: a community perspective

Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.