Validation of biomacromolecular structures determined by NMR spectroscopy and deposited in the Protein Data Bank

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Protein Data Bank in Europe

Abstract

The proposed research addresses the quality of 3D structures of important biological molecules such as proteins, nucleic acids and their complexes. Knowledge of these structures is essential in many areas of science and helps us understand the molecular basis of life and disease processes, design better drugs, improve the efficiency of enzymes used in the food, paper or agriculture industry, etc. Structural data is archived in a single, freely accessible, global archive called the Protein Data Bank (PDB). The structural information is deposited in the PDB by academic and industrial researchers from all over the world and is used by other scientists to advance our knowledge and understanding of human health, drug discovery, agriculture, etc. Every month, more than 25 million PDB structure files are downloaded from the websites of the four organisations that manage the PDB, the wwPDB consortium. Of more than 73000 entries in the PDB, about 86% were determined using a technique called X-ray crystallography, while 13% come from Nuclear Magnetic Resonance (NMR) spectroscopy.

Structure determination by NMR typically involves weeks of data collection and manual analysis of complex spectra. As with any experimental technique, NMR structures may contain errors. To ensure that the data deposited in the PDB are reliable, there is a need for comprehensive validation, which tells both producers and users of structures how good (or bad) their structures are, both in absolute terms and compared to other structures. This helps NMR spectroscopists to produce better models, and structure users in academia or industry to better judge the quality of the data they want to use or to select the best data for their purposes. To address this issue, expert validation task forces (VTFs) have been set up by the wwPDB, which will recommend what validation methods should be used and which areas still require further research.

Our aim is to improve validation of NMR-derived structures. The objectives of this proposal are:
1. To implement the recommendations of the NMR VTF in an integrated software pipeline. This pipeline will be used to assess the quality of all NMR structures already in the PDB and of all structures that will be deposited in the future.
2. To critically assess the utility, scope and limitations of current NMR validation tools. This will reveal why current validation methods sometimes fail, amongst other things.
3. To develop new algorithms, procedures and tools for validation of NMR structures. Any limitations and weaknesses identified in the previous step will be addressed here.
4. To disseminate validation-related information and newly developed validation methods for use by the wider scientific community. This ensures that NMR spectroscopists will be able to produce better models, and that non-expert users will be able to assess the quality of NMR structures available to them.

One applicant, Prof. Kleywegt is head of the Protein Data Bank in Europe (PDBe). PDBe is a founding member of the wwPDB and is part of the European Bioinformatics Institute, a world leader in bioinformatics research and services. PDBe has extensive expertise in all major structure determination techniques and is already implementing the recommendations of the wwPDB X-ray VTF. The co-applicant , Prof. Vuister, is part of the Department of Biochemistry of the University of Leicester (UoL), home to 3 NMR- and 2 X-ray groups. He is a leading expert on validation of NMR-derived structures and is a member of the NMR VTF.

Technical Summary

NMR structures in the Protein Data Bank (PDB) contain errors that often go undetected. The errors originate from limited data quality and quantity and complex computational procedures, as well as inherent dynamics of the biomacromolecules. There is currently no extensive mandatory validation of NMR structural data before deposition to the PDB and BMRB, nor is there a complete understanding of the limitations of current validation servers (CING and PSVS).

The clear need for improved NMR-derived biomacromolecular structures forms the basis of the four objectives for this proposal:

1. To implement the recommendations of the wwPDB NMR Validation Task Force (VTF) into an integrated software pipeline. This work will build upon the X-ray validation pipeline currently under development at PDBe. The pipeline will allow for validation of structures prior to deposition to the PDB and BMRB and will be used by all wwPDB partners. In addition, the pipeline will be used to assess the quality of all NMR structures in the PDB and the results will be made freely available.
2. To critically assess the utility, scope and limitations of current NMR validation tools. This work will build on the results of Objective 1 as well as prior research in the Vuister group using the CING validation software.
3. To develop new algorithms, procedures and tools for validation of high-resolution NMR structures, addressing issues such as dynamics and sparse data.
4. To disseminate validation-related information as well as newly developed validation methods for use by the wider scientific community. This will include development of new visualisation services at PDBe to help expert and non-expert users assess the quality of any NMR structure in the PDB. It will also include development of new publicly-available validation tools at Leicester.

PDBe will be the scientific lead for work on Objectives 1 and 4, and Leicester for work on Objectives 2 and 3.

Planned Impact

Structure determination and the study of interactions using biomacromolecular NMR techniques is still a rapidly growing field, with many new applications being developed all the time. Both automation and integrated pipelines have gradually changed the structure determination process from a highly expert undertaking to a more routine tool for biological research, albeit one that still requires dedicated technical expertise.

The current proposal addresses an important aspect of the structure determination process: validation of the resulting models in relation to both prior knowledge (chemical, physical and biological) and specific experimental data collected on a sample containing the molecule(s) of interest. Careful validation often allows detection and remediation of potential problems commonly encountered for NMR-derived structures. As a result, more reliable NMR structures will be obtained. We expect that the present project will contribute significantly to (a) quality improvement of all biomacromolecular NMR structures to be deposited in the PDB in the future, and (b) awareness of the quality of all existing NMR structures in the PDB (13% of the archive). These structures will then form a better starting point for understanding their biology, for protein engineering, homology modeling and drug design. The results of the project will strengthen the UK scientific innovative capacity and fit the BBSRC research priority "Technology development for bioscience". The users will include researchers at academic and government institutions, industrial laboratories as well as students and teachers with an interest in structural biology.

The tools, information and resources produced in this project will become widely available, as both partners have extensive experience in the development of web-based services. It is the mission of PDBe to curate newly deposited structures and to provide structural data and advanced services and resources to the worldwide scientific and industrial community. Their web servers, part of the EBI data centres, process millions of requests every month. The NMR group at the University of Leicester has been at the forefront in the development of validation tools. Their dedicated iCing validation server will be expanded to accommodate the new tools. The server already performs over 1000 validation runs on a yearly basis with requests originating from all continents, except Antarctica, and demand is still increasing. User input will provide important feedback regarding the general applicability and usability of our tools.

Both applicants participate in many international collaborations. PDBe is a partner in the Worldwide PDB consortium and EMDataBank and has participated in many EU-funded projects. While previously located in Nijmegen, the NMR-validation research program now at the University of Leicester was and is a participant in many EU-funded NMR-oriented projects, such as WeNMR. The latter effort is aimed at the development of a virtual research community (VRC) that will strengthen biomacromolecular NMR as a tool in biological research. The proposed research will both benefit from and strengthen this EU effort, as the WeNMR VRC will be an excellent platform for the dissemination of some of the results of the project.

The post-doctoral researchers for whom support is requested here, will work in an international and scientifically excellent research environment. The project will require them to utilise and develop their technical, scientific and personal skills. It is expected that the interactions within the respective groups in Hinxton, Leicester and Nijmegen will also raise awareness of the project with other post-doctoral researchers and graduate students active in the structural biology field. In fact, these researchers comprise an important target group of users of the tools that will be developed in the project.

Publications

10 25 50

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Berman HM (2016) The archiving and dissemination of biological structure data. in Current opinion in structural biology

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Burley SK (2017) Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. in Methods in molecular biology (Clifton, N.J.)

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Gutmanas A (2015) NMR Exchange Format: a unified and open standard for representation of NMR restraint data. in Nature structural & molecular biology

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Gutmanas A (2014) PDBe: Protein Data Bank in Europe. in Nucleic acids research

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Gutmanas A (2013) The role of structural bioinformatics resources in the era of integrative structural biology. in Acta crystallographica. Section D, Biological crystallography

 
Description The principal goals of the project were:
1. Development and implementation of the software pipeline to validate NMR structures and data deposited to the PDB. The pipeline has been in production since early 2016.
2. Development of web-based tools for the visualisation and presentation of the validation data to the visitors of PDBe website. A prototype tool (Vivaldi) has been deployed.
Exploitation Route The validation pipeline for NMR structures in the PDB is being enhaced by the wwPDB partnership to support additional data types. All wwPDB partners now expose this data in a variety of ways on their websites.
Sectors Agriculture, Food and Drink,Chemicals,Education,Pharmaceuticals and Medical Biotechnology

URL https://deposit.wwpdb.org
 
Description NEF working group 
Organisation ETH Zurich
Country Switzerland 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Free University of Brussels
Country Belgium 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Lawrence Berkeley National Laboratory
Country United States 
Sector Public 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation National Institutes of Health (NIH)
Country United States 
Sector Public 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Osaka University
Country Japan 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Pasteur Institute, Paris
Country France 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Rutgers University
Country United States 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Rutgers University
Country United States 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation Technical University of Munich
Country Germany 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation University of Alberta
Department Department of Biological Sciences
Country Canada 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation University of Leicester
Department Department of Molecular and Cell Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation University of Valencia
Country Spain 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation University of Wisconsin-Madison
Country United States 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Description NEF working group 
Organisation École normale supérieure de Lyon (ENS Lyon)
Country France 
Sector Academic/University 
PI Contribution PDBe, its wwPDB partners and University of Leicester have convened an initial workshop of software developers (PIs) in the field of NMR to devise a unified way to represent the NMR restraints. PDBe hosted the workshop and participated in the discussions. The community agreement on a new format to represent the restraints data was reached at the workshop and refined in a series of subsequent virtual and face-to-face meetings. PDBe took the lead in publishing the first outcome of the effort - the NMR exchange format (NEF).
Collaborator Contribution All partners contributed expertise and offered solutions to the problem of NMR restraint representation. All partners agreed to adopt the new format (NEF) and modified their software to both export and import data in NEF. The wwPDB partners (including PDBe) have facilitated the interactions and are planning to update the NMR deposition, annotation and validation software to support NEF-formatted data files.
Impact Paper: Gutmanas et al., NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol (2015) 22:433-434. doi:10.1038/nsmb.3041
Start Year 2013
 
Title OneDep deposition and biocuration system 
Description The OneDep deposition and biocuration system is deployed at all wwPDB deposition sites and integrates validation pipeline as part of data submission, curation and release. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact The NMR validation pipeline was integrated into OneDep in 2016. 
 
Title Vivaldi - Visualisation and validation display 
Description Vivaldi is a PDBe webservice, which allows both expert and non-expert users to visualise NMR structures deposited in the PDB archive as well as available validation reports. 
Type Of Technology Webtool/Application 
Year Produced 2011 
Impact To date, the Vivaldi tool received 4 citations on peer review papers. Underlying infrastructure has been used to continue our group's work in the validation of NMR entries in the PDB. There are more than 250 unique visitors to the Vivaldi page each month. 
URL http://pdbe.org/vivaldi
 
Title stand-alone validation server 
Description The stand-alone validation server allows structural biologists to obtain preliminary validation reports prior to submission. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact From 2016, the server allows upload of NMR structures and chemical shifts, in addition to crystallographic structures. 
URL http://validate.wwpdb.org
 
Title wwPDB NMR structure validation pipeline 
Description The wwPDB partners developed a validation pipeline, which is now integrated into the wwPDB deposition and biocuration system - OneDep. It provides validation reports at the time of submission, biocuration and public release of PDB entries. It includes most of the recommendations of the wwPDB NMR validation task force (VTF). OneDep is deployed at all wwPDB deposition sites - PDBe, RCSB PDB and PDBj. 
Type Of Technology Software 
Year Produced 2016 
Impact The resulting validation reports are now available for all publicly released PDB entries determined by NMR spectroscopy. 
URL http://wwpdb.org/validation/validation-reports
 
Description CEITEC Winter School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Two invited lectures:

• "The wonderful world of structure archiving - What's happening and what's next?", invited lecture, CEITEC Winter School on Structural Cell Biology, Brno, Czech Republic, February 2015.

• "Applied common sense - The why, what and how of validation", invited lecture, CEITEC Winter School on Structural Cell Biology, Brno, Czech Republic, February 2015.
Year(s) Of Engagement Activity 2015
 
Description CSHL course: X-Ray Methods in Structural Biology 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited lecture as well as two practicals and discussions with students in the course and fellow course instructors.
Year(s) Of Engagement Activity 2016
URL http://meetings.cshl.edu/courses.aspx?course=c-crys&year=16
 
Description Cambridge science festival volunteer 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Multiple opportunities to engage with the members of the public, primarily parents of schoolchildren, and explain basics of structural biology and its possible applications.

There were inquiries from science teachers about these and similar activities to enrich their teaching curriculum.
Year(s) Of Engagement Activity 2013
 
Description Invited lecture at Pasteur Institute, Paris, July 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited lecture at the Integrative Structural Biology advanced course in 2017 and in 2018. The purpose was to present wwPDB and PDBe work on supporting integrative/hybrid methods for data deposition and data access. I also presented the work done on validation of structures and in 2018 I conducted a short tutorial on NMR validation. The lecture and tutorial were well received, and our team already received an invitation to participate in the upcoming course in 2019 with a somewhat more generous time allocation for our contribution.
Year(s) Of Engagement Activity 2017,2018
URL https://www.pasteur.fr/en/integrative-structural-biology
 
Description Invited speaker talk on Structural Biology Data Archiving at FEBS Congress 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact "Structural biology data archiving - where are we and what lies ahead?", invited lecture, FEBS Congress, Prague, Czech Republic, July 2018.
Year(s) Of Engagement Activity 2018
 
Description Lecture on Structural Biology Data Archiving 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact "Structural biology data archiving - where are we and what lies ahead?", seminar, EMBL, Heidelberg, Germany, September 2018.
Year(s) Of Engagement Activity 2018
 
Description Lecture titled Just because it is in Nature, does not mean it is true 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact This lecture titled 'Just because it's in Nature, doesn't mean it's true', was presented as part of the course on X-ray Methods in Structural Biology, at the Cold Spring Harbor Laboratory, NY, USA.
Year(s) Of Engagement Activity 2017,2018
 
Description Lecture: Practical NMR Course, Swedish NMR Centre 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The lecture and computer practical made the students think about the importance of critical assessment of their results and showed which validation tools are available .

The students left the course more aware of which software tools to use when assessing their or other researchers' results.
Year(s) Of Engagement Activity 2014
 
Description NMR practical course - Gothenburg - Sep 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Within the context of a practical course on NMR spectroscopy, approximately 15 graduate students and 10 senior academics attended a presentation and a practical session on validation of experimental NMR data and NMR-derived structures. Approximately 5 of the students submitted a written report on the practical which allowed them to receive appropriate credits from the course.
Year(s) Of Engagement Activity 2017
URL https://nmr.gu.se/digitalAssets/1656/1656869_program_20170905.pdf
 
Description Protein Structure Determination in Industry Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Keynote speaker at the Protein Structure Determination in Industry Conference in Malmö, Sweden. Interacted with the other participants, most of whom are in pharma and biotech companies.
Year(s) Of Engagement Activity 2016
URL http://psdi2016.org/index.html
 
Description Seminar in Uppsala 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited lecture and follow-up discussion with local scientists and students.
Year(s) Of Engagement Activity 2016
 
Description Seminar in Vienna 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited lecture on "The wonderful world of structure archiving - what's happening and what's next?" as well as discussions with various local scientists and students.
Year(s) Of Engagement Activity 2016
 
Description Structural bioinformatics training course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Co-organiser of and lecturer in this practical course, interacting with students and fellow instructors.
Year(s) Of Engagement Activity 2016,2017,2018
URL http://www.ebi.ac.uk/training/events/2016/structural-bioinformatics-2016
 
Description Talk and tutorial at CCPN conference 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact About 20 graduate students and postdocs and a few senior scientists attended a CCPN workshop on NMR data management. A. Gutmanas presented the wwPDB NMR validation reports and offered a tutorial on how these reports should be read and understood.
Year(s) Of Engagement Activity 2015
URL http://www.ccpn.ac.uk/meetings/upcoming-meetings/ccpn-conference-buxton-2015/pre-conference-workshop...
 
Description Talk at EMBO Workshop on Magnetic resonance 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation paper presentation
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk led to further discussion, which highlighted the need of validation of nucleic acids and not only protein structures.

It is premature to judge the impact beyond the immediate audience
Year(s) Of Engagement Activity 2014
 
Description Talk at Euromar 2015 - NMR structure validation reports 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at a parallel session at the EUROMAR conference in 2015. EUROMAR is the largest yearly European scientific conference in field of magnetic resonance. The audience was about 200 scientists at all levels of their careers. A number of questions were asked were followed up by private discussions during breaks.
Year(s) Of Engagement Activity 2015
URL http://www.euromar2015.org/
 
Description Univ of Copenhagen PhD Day (keynote speaker) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Keynote speaker at the PhD Day of the Dept of Biology of the Univ of Copenhagen. Also interacted with students who presented posters as well as the PhD students who organised the PhD Day.
Year(s) Of Engagement Activity 2016
URL http://phdday.wixsite.com/2016
 
Description Update to NMR VTF 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact PHx presented to the NMR VTF the progress of the wwPDB NMR validation pipeline: well-defined vs ill-defined regions (June), large-scale analysis of knowledge-based validation of NMR structures (June) and prediction of chemical shifts (November).

The VTF based its choice on the method to identify the well-defined regions of proteins based on this report.
Year(s) Of Engagement Activity 2013
 
Description Workshop on unified representation of NMR restraints 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact An agreement on the unified representation of NMR restraints was reached and a working group constituted.

The leading software developers in structural NMR agreed on their software reading and writing the new agreed-upon format for NMR restraints and related data.
Year(s) Of Engagement Activity 2013