wwPDB 2024 News

04/08/2024

CASP16 Call for Targets

CASP (Critical Assessment of protein Structure Prediction) is in search for targets.

CASP (Critical Assessment of protein Structure Prediction) experiments are held every two years. Recent rounds have seen dramatic increases in modeling accuracy, resulting from the introduction of deep learning methods: In 2018, for the first time, the folds of most proteins were correctly computed [1]; in 2020, the accuracy of many computed protein structures rivaled that of the corresponding experimental ones [2]; in 2022, there was an enormous increase in the accuracy of protein complexes [3].

We have seen the beginning of what deep learning methods may achieve in structural biology. In addition to further increases in the accuracy of protein complexes, methods are being developed for RNA structures, organic ligand-protein complexes, and for moving beyond single macromolecular structures to compute conformational ensembles. Accurate computational methods together with experimental data also offer the prospect of probing previously inaccessible biological systems. CASP has expanded its scope to provide critical assessment in all these areas.

CASP is only possible with the generous participation of the experimental structural biology community in providing suitable targets: A total of over 1100 targets have been obtained over the previous CASP rounds. We are now requesting targets for the 2024 CASP16 experiment. We need challenge targets in the following areas:

Single protein structures: The 2020 and 2022 CASPs showed that, so far, Alphafold2 and methods built around it are by far the most accurate [4]. But there are limitations, particularly for some proteins where only a shallow sequence alignment is available and for very large proteins (more than 1000 amino acids). The best results also require substantial amounts of computing resources, well beyond that of the AlphaFold2 default settings. Many new methods are continuing to appear and these may remove some of the remaining difficulties. All types of protein targets are needed, but especially those with shallow sequence alignments, without structural templates, and large proteins.

Protein complexes: In the 2022 CASP15, advanced deep learning methods were applied to protein complexes for the first time [5]. The result was a huge improvement in accuracy compared with classical docking approaches. But overall, the results are still not at the level achieved for single proteins. So, in CASP16 we need all sorts of targets in this area so as to determine progress since then. We particularly need complexes where there is no evolutionary information across the protein-protein interfaces, for example, antibody-antigen complexes. (This CASP category is conducted in close collaboration with our colleagues at CAPRI - Critical Assessment of protein interactions [6]).

Nucleic acid structures and complexes: In recognition of the major role nucleic acid structures and complexes play in biology, CASP now includes this class of target. A number of papers claiming successful RNA structure computation using deep learning methods have been published, but those participating in the 2022 CASP RNA category performed less well than classical approaches, and no methods were able to effectively address the two RNA protein-complexes included [7]. CASP needs a wide variety of RNA, DNA, and complexes as targets to see if this situation has changed. (This CASP category is conducted in close collaboration with RNApuzzles [8]).

Organic ligand-protein complexes: This area is of major importance for computer-aided drug discovery. Earlier, there have been community experiments to assess the accuracy of methods, particularly SAMPL, CSAR, D3R, and a new one, CACHE, has recently started. These challenges have drawn strong international participation from researchers in both academia and industry. Here too, a number of promising deep learning papers have appeared, but in the 2022 CASP15 pilot, classical methods were still superior [9]. So, we need appropriate targets to see if progress has been made since. Ideally, these should be sets of three-dimensional protein-ligand complexes from drug discovery projects, but single targets would also be appreciated. Additionally, where available, we will assess non-structural quantities such as affinities or affinity rankings and other properties of pharmaceutical interest when these are available (small molecule pKs, and DMPK related properties).

Ensembles of macromolecule conformations: It is now widely recognized that proteins and nucleic acids often adopt multiple conformations that can underpin their functions. In these cases, considering only a single protein or RNA conformation may be a significant oversimplification. The 2022 CASP15 included a pilot experiment to assess methods for computing multiple conformations, with encouraging results [10], but with limitations imposed by the available experimental data. For 2024, we seek not only cases of multiple experimental three-dimensional structures for the same macromolecule but also other types of data that might be used for assessment of computed conformation ensembles such as cryoEM, NMR, X-ray crystallography, SAXS, and/or cross-link data.

Integrative modeling: The more powerful computational methods open up new possibilities for combination with sparse or low-resolution experimental data to investigate previously inaccessible biological structures and machines. CASP is interested in exploring these possibilities and so requests experimentally difficult targets where structure has nevertheless been obtained. In appropriate cases, we expect to be able to collaborate with other experimental groups to provide appropriate data from NMR, cross-linking or SAXS.

There are three avenues to contribute a target to CASP:

1. (preferred) Submit directly to CASP through our web-interface (requires a quick registration if you do not have an account with us).
2. Email to targets@predictioncenter.org with your target suggestions or to discuss any questions.
3. Submit your structure to the PDB (on-hold) and designate it as a CASP target through PDB’s submission interface.

The timeline for the 2024 CASP requires that targets are submitted starting now and until July 1. We would like to hear from you as soon as possible if you may have something suitable or have suggestions about other target sources. In order to maintain rigor, the experimental data for a target must not be publicly available until after computed structures have been collected. For assessment, CASP requires the experimental data by August 15, but the data can remain confidential after that. Target providers are invited to contribute to papers [11-15] for a special CASP issue of the journal Proteins.

CASP organizers: John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Maya Topf

1. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 2019;87(12):1011-1020.
2. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIV. Proteins 2021;89(12):1607-1617.
3. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XV. Proteins 2023;91(12):1539-1549.
4. Simpkin AJ, Mesdaghi S, Sanchez Rodriguez F, Elliott L, Murphy DL, Kryshtafovych A, Keegan RM, Rigden DJ. Tertiary structure assessment at CASP15. Proteins 2023;91(12):1616-1635.
5. Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins 2023;91(12):1636-1657.
6. Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin A, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91(12):1658-1683.
7. Das R, Kretsch RC, Simpkin AJ, Mulvaney T, Pham P, Rangan R, Bu F, Keegan RM, Topf M, Rigden DJ, Miao Z, Westhof E. Assessment of three-dimensional RNA structure prediction in CASP15. Proteins 2023;91(12):1747-1770.
8. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res 2020;48(2):576-588.
9. Robin X, Studer G, Durairaj J, Eberhardt J, Schwede T, Walters WP. Assessment of protein-ligand complexes in CASP15. Proteins 2023;91(12):1811-1821.
10. Kryshtafovych A, Montelione GT, Rigden DJ, Mesdaghi S, Karaca E, Moult J. Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins 2023;91(12):1903-1911.
11. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins 2023;91(12):1600-1615.
12. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markusson S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Jr., Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023;91(12):1571-1599.
13. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Bottcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021;89(12):1647-1672.
14. Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Jr., Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019;87(12):1037-1057.
15. Kryshtafovych A, Albrecht R, Basle A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes C, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018;86 Suppl 1(Suppl 1):27-50.

03/21/2024

Paper Published on NMR Restraint Validation

We are pleased to announce the publication of this manuscript, addressing the challenge of validation of experimental biomolecular NMR structures against restraint data.

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 harvesting 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.

We present the rationale for model-vs-data restraint validation by the wwPDB, together with summary of validation tools and reports for NMR distance and dihedral restraints that have been developed, as implemented in the wwPDB validation pipeline and recommended by the wwPDB NMR-VTF committee.

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin Bardiaux, Charles Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, Gaetano T Montelione, Geerten W Vuister, Jasmine Y Young
(2024) Structure 32, 1–14: doi: 10.1016/j.str.2024.02.011

The wwPDB plans to further enhance validation report by providing model-vs-data quality assessment for other kinds of restraints based on community recommendation and improve data representation on structures with multiple conformation states.

03/12/2024

Paper Published on CryoEM Archiving and Validation Recommendations

A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and setting community recommendations. The outcomes of this meeting have now been published in this manuscript which highlights the recent achievements made by the wwPDB in the space of 3DEM validation and the community recommendations going forward. Some of these recommendations have already been implemented, such as a three-tiered strategy powered by the Validation Analysis (VA) pipeline for the dissemination of validation information and ensuring the that VA can be run by external applications.

Community recommendations on cryoEM data archiving and validation
Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H.W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
(2024) IUCrJ 11: 140–151 https://doi.org/10.1107/S2052252524001246

Graphical Abstract

03/06/2024

Poster Prize Awarded at The Biophysical Society Meeting

The wwPDB Foundation made an award for outstanding student presentations at the 2024 Biophysical Society Meeting (February 10-14, Philadelphia, PA).

Irin Pottanani Tom

Mechanisms of Light Signalling and Allosteric Regulation in Dual Sensor Photoreceptor PPHK
Irin Pottanani Tom (1), Heewhan Shin (1), Chang Liu (2), Indika Kumaeapperuma (1), Zhong Ren (1), Minglei Zhao (1), Xiaojing Yang (1)
1) University of Illinois at Chicago, 2) University of Chicago

Many thanks to The Biophysical Society organizers and poster prize judges for making this award possible.

The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

The wwPDB Foundation is grateful for our industrial sponsors: Discngine, OpenEye Scientific, Roivant Sciences, Rigaku, and ThermoFisher Scientific. Individual sponsorships are also available.

Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation.

02/27/2024

Latest Developments on the EMDB Published

This manuscript addresses the recent developments in the archiving of 3DEM data and the future plans for the EMDB. The burgeoning popularity of the electron microscopy field has been coupled with new technologies and software solutions, together this has pushed exponential growth in yearly depositions, increases in the resolution of the deposited data, and, consequently, accuracy of molecule models associated with 3DEM data. As the EMDB continues to grow it remains dedicated to delivering a world-class archive that adheres to FAIR principles. In addition, we recognise the importance of easy and open access to accurately curated data for the various users of the archive, we plan to continue to facilitate and enhance this moving forward.

EMDB—the Electron Microscopy Data Bank
The wwPDB Consortium
Nucleic Acids Research (2024) 52: D456–D465 https://doi.org/10.1093/nar/gkad1019

02/11/2024

Biocurator Milestone: >10,000 Depositions Processed

Congratulations to biocurator Minyu Chen on processing over 10,000 PDB depositions. She is the second biocurator to reach this milestone in the PDBj and the fifth in the wwPDB. Yumiko Kengaku reached this milestone in April 2021.

Minyu received her PhD in Environmental Engineering from Osaka University and joined PDB after working at the National Cerebral and Cardiovascular Center, Osaka. She has joined PDB in 2007 and is now working at the branch office of PDBj in the Protein Research Foundation, Osaka. She has established herself as a highly qualified professional with deep understanding of scientific data and various experimental techniques and dedication to exceptional quality data curation. Her profound data curation expertise and commitment to excellence contributed to the high quality data archive for the benefit of the scientific community. We congratulate Minyu with this exciting accomplishment and look forward to her future success.

Chairman of the Protein Research Foundation, Prof. Toshiharu Hase, and Dr. Minyu Chen.

Milestone tumbler.

02/05/2024

Preprint Published on NMR Restraint Validation

Graphical Abstract

This manuscript addresses this challenge of validation of experimental biomolecular NMR structures against restraint data. 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 harvesting 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. We presented the rationale for model-vs-data restraint validation by the wwPDB, together with summary of validation tools and reports for NMR distance and dihedral restraints that have been developed, as implemented in the wwPDB validation pipeline and recommended by the wwPDB NMR-VTF committee.

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin Bardiaux, Charles Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, Gaetano T Montelione, Geerten W Vuister, Jasmine Y Young
(2024) bioRxiv 2024.01.15.575520; doi: 10.1101/2024.01.15.575520

wwPDB plans to further enhance validation report by providing model-vs-data quality assessment for other kinds of restraints based on community recommendation and improve data representation on structures with multiple conformation states.

02/01/2024

Preprint Published on CryoEM Archiving and Validation Recommendations

The number of released EMDB entries per year in a number of resolution bins, from 2010 until December 2023

A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and set community recommendations.

Community recommendations on cryoEM data archiving and validation
Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H.W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
(2023) arXiv doi: 10.48550/arXiv.2311.17640

Several community recommendations from this workshop have been incorporated into wwPDB validation reports including map analysis, FSC validation, and map-model fitness using Q-score. wwPDB plans to provide overall quality percentile on map-model fitness compared to other PDB entries in the wwPDB validation report as the next step.

01/29/2024

Preprint Published on NextGen Archive

A new paper describes how the recently-announced NextGen Archive provides centralized access to integrated annotations and enriched structural information for PDB data:

NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank
Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley
(2023) bioRxiv doi: 10.1101/2023.10.24.563739

The PDB NextGen archive provides sequence annotation from external resources such as UniProt, SCOP2 and Pfam in addition to the content provided in the structure model files in the PDB main archive. The inclusion of UniProtKB numbering facilitates effortless structural comparisons between experimental and predicted protein models. These PDBx/mmCIF files are directly compatible with various data visualization tools, simplifying the display of annotations on 3D structure views.

01/28/2024

Prizes Awarded at The Biophysical Society Japan Meeting

The wwPDB Foundation made awards to outstanding student presentations at the 2023 The Biophysical Society Japan Meeting (November 14-16, Nagoya, Japan).

Keisuke Kasahara

Thermodynamic analysis of Fv-supercharged antibody–antigen interactions and control of interaction parameters
Keisuke Kasahara (1), Daisuke Kuroda (2), Jose Caaveiro (3), Satoru Nagatoishi (4), Kouhei Tsumoto (1,4)
1) Dept. Bioeng., Grad. Sch. Eng., Univ. Tokyo; 2) Res. Ctr. Drug Vaccine Dev., NIID; 3) Grad. Sch. Pharm. Sci., Kyusyu Univ., 4) Med. Dev. Dev. Reg. Res. Ctr., Grad. Sch. Eng., Univ. Tokyo

Kyle Ian Peter Le Huray

Harnessing the power of machine learning and high-throughput molecular dynamics simulations to predict protein-lipid interactions Kyle Ian Peter Le Huray (1,2), Frank Sobott (1), He Wang (3), Antreas Kalli (2)
1) School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK; 2) Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; 3) School of Computing, University of Leeds, Leeds, UK

Katsuhiko Minami

Replication-dependent histone (Repli-Histo) labeling revealed that chromatin motion can determine DNA replication timing
Katsuhiko Minami (1,2), Satoru Ide (1,2), Sachiko Tamura (1), Masato T. Kanemaki (1,2), Kazuhiro Maeshima (1,2)
1) National Institute of Genetics; 2) Graduate Institute for Advanced Studies, SOKENDAI

Many thanks to the meeting organizers and prize judges for making these awards possible.

The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation.

01/08/2024

Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

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01/03/2024

Time-stamped Copies of PDB and EMDB Archives

New archive snapshots are available.

A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org, https://s3.rcsb.org) as of January 2, 2024 has been added to ftp://snapshots.wwpdb.org, https://s3snapshots.rcsb.org (AWS), and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20240101 includes the 214,121 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 1,242 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 01, 2024 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20240101/ and ftp://snapshots.pdbj.org/20240101/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (32,033 and 282, respectively) and is 14 TB in size.