An integrative approach to deciphering the entry process in Herpesviruses

Lead Research Organisation: Birkbeck College
Department Name: Biological Sciences

Abstract

Cellular processes are governed by the intricate coordination and dynamics of biological macromolecules called proteins and nucleic acids. These do not act in isolation but rather interact with each other and assemble to form cellular complexes. Understanding the structures of complexes can be an important step not only in understanding basic cell biology but also disease, as such complexes are also formed between the proteins of invading pathogens like viruses and the host cell proteins. Indeed, to determine how a virus functions, knowledge is needed not only about the molecular arrangement of its own proteins but also about their interactions with the host cell over the course of the viral life cycle. Particularly interesting is the entry process, the earliest stage of infection in the cycle, when the virus comes into first contact with the host cell and introduces viral material into the cell. The goal of our project is to gain a structural view of the entry process in one of the largest and most complex families of viruses that infect humans - the Herpesviruses. The severity of conditions caused by these viruses ranges from cold sores, genital ulcers, and blisters to blindness and life-threatening conditions including fatal encephalitis, meningitis and cancer. This family constitutes a major public health concern due to their worldwide prevalence, ease of spread, and severity of the associated symptoms. To achieve this, we propose a multi-disciplinary approach that integrates computational and experimental methods.

The field that aids this project is Structural Biology. It provides 'pictures' of macromolecular complexes and their components through the use of experimental techniques such as X-ray crystallography and nuclear magnetic resonance, each of which has its own limitations to what it can accomplish, depending on the size and purity of sample under investigation, the conditions in which its prepared, and the homogeneity of the complex it contains. In the last decade, cryo electron microscopy and tomography have also become important techniques for observing biological complexes. With these techniques, samples are rapidly frozen using cryogenic liquids and then bombarded with electrons, yielding many images of the 2-dimensional sample that can be combined into a clearer 3-dimensional picture. In tomography, such pictures can provide the overall organization of cells and tissues, and can capture pathogens during cell invasion. They contain many different macromolecular complexes that can be detected in their native environment. Though these techniques have led to many interesting discoveries, here too there are limitations, typically not resulting in near-atomic pictures.

In this project, we will study the entry process in human herpesviruses. To this end, we will develop a computational approach that pulls together information from a variety of experimental techniques to construct a clearer and more complete description of structures of complexes imaged initially by cryo electron tomography. The method will have the capability of incorporating information about which protein interacts with which (or how close they are to each other). Such information could come from a variety of techniques, often grouped under the name 'proteomics'. Together, we will fit all the different pieces of information like a jigsaw puzzle, creating a higher resolution picture of the visualised complexes. Obtaining the structures of selected complexes (formed between the proteins placed on the envelope of the virus and between them and their interacting proteins from the host cell) will represent a major advance in our understanding of the molecular and mechanistic details of herpesvirus pathogenesis. This will allow us to improve current models of the entry process, a crucial step towards identifying drug targets. Our novel approach will be applicable to many viral systems and will open the door for similar studies on other pathogens.

Technical Summary

A detailed description of the structures of macromolecular complexes can be very valuable for understanding cellular processes, including those that are targeted and modified by pathogens. However, due to current limitations of experimental techniques, the only way to achieve a comprehensive characterisation of these structures is to adopt an integrative approach that combines information from multiple sources. At present there are very few methods attempting to do so systematically. Here we aim to integrate multiple experimental and computational approaches to characterise complexes formed between herpesviruses and their host during the entry stage of infection.

The field of 3D EM is increasingly important in molecular and cellular biology, owing to advances in hardware and software that improve image quality and experimental efficiency. One advantage is that the resulting maps often correspond to large and heterogeneous complexes that are difficult to study by other techniques. In tomography in particular, new biological insights arise from structure determination of macromolecular machinery in the native cellular context (here membranes).

Here, we propose to build on Topf group's previous work on data integration and develop a method that efficiently and accurately combines the structures of individual components with low-resolution maps of the complexes they form. These maps will result from cryo electron tomography combined with sub-tomogram averaging and classification performed in the Grünewald lab. The method will allow the inclusion of additional spatial information from chemical cross-linking coupled with mass spectrometry and protein-protein interaction (PPI) networks. The resulting models of sub-complexes mediating herpesvirus entry could potentially lead to the discovery of novel functional details about the infection process. Additionally the Grünewald group will continue to refine image data acquisition and image processing tools and pipelines.

Planned Impact

Who will benefit from this research?

The proposed research will potentially generate knowledge of value to (i) the wider bioscience and biomedical communities; (ii) the pharmaceutical industry; and (iii) the general public and government policy makers (e.g., national health and overseas aid).

How will they benefit from this research?

The main contributions from this research will be to (i) elucidate the structure of novel complexes formed during the entry process of herpesviruses and (ii) to provide computational tools and experimental protocols for generating such structures by integration of data from 3D electron microscopy, mass spectrometry and protein interaction networks. In the long term, applying the methods to as many biological complexes as possible will help to generate more fundamental knowledge about basic cell biological processes. This systems level analysis of biological processes is particularly important at the moment, where there is a lot of knowledge about structures and functions of individual proteins, but much less on how they work together in the cellular context. Such information can have valuable implications to the immediate bioscience community.

Additionally, the immediate goal is also to apply the methods to decipher structures of complexes formed between herpesviruses and their host cells. Information generated from such studies is directly related to the understanding of infection and disease and therefore will be of interest to the general public and the pharmaceutical industry. The results on HCMV could reveal new insights into spread of the virus (which presents a particular threat to newborns) and identify new drug targets, which will be beneficial not only to the biomedical community and pharmaceutical industry, but also to the public sector and government policy makers (e.g., national health services and overseas aid). Understanding how herpesviruses work in general is of great importance for improving quality of life and human health, with 5 of the 8 members of the family affecting more than 90% of adult population worldwide. Knowledge about the first step in the infection by these viruses is key to identifying new drug targets and/or to develop a vaccine. This is of high relevance not only for basic researchers but also pharmaceutical industries and the general public. Such contribution could impact the economic competitiveness of the UK in pharmaceutical research and economic development. Ultimately, the results could impact clinicians and patients, through availability of more effective treatments, as well as government policy makers (e.g., in relation to the national health services). Given the importance of diseases caused by the herpesviruses family in developing nations the research could also impact foreign policy decision-makers regarding overseas aid agencies.

The communication about the integrative approach to structural biology and new insights resulting from the research (through the long-term application of the proposed methods to many complexes), whether related to basic cell biology or disease, could all have an impact on the public education of science and arts. This will be done via websites and challenges (e.g., http://autopack.cgsociety.org/autopack/), books and museums.

Finally, highly skilled researchers working on the proposed project will be trained in transferring scientific knowledge to the public and the preparation of materials for communication (e.g., via publications, user-friendly web interfaces, and software documentation). They will participate in professional seminars organised at STRUBI and ISMB, and in seminars on communicating sciences to the public in the centre for learning and professional development (at our universities). They will also be directly involved in the research collaborations. These acquired skills will contribute to the development of their future career not only in bioscience but rather in all employment sectors.

Publications

10 25 50
 
Description Modelling the entry process in Human Cytomegalovirus using genomics from natural populations
Amount £70,000 (GBP)
Organisation Bloomsbury Colleges 
Sector Academic/University
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description Timestamping Integrative Approach to Understand Secondary Envelopment of Human Cytomegalovirus
Amount £673,700 (GBP)
Funding ID 209250/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2018 
End 03/2023
 
Title Flex-EM for high resolution EM 
Description We improved the Flex-EM method to make it applicable for refinement of high-resolution 3D electron microscopy maps 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact We have used the method to refine a number of new structure, in particular GroEL and microtubule-bound complexes. 
URL http://topf-group.ismb.lon.ac.uk/flex-em/
 
Title Validation toold for models in cryoEM maps - TEMPy 
Description We developed new scores for validation of atomic models in cryoEM maps, we also added features for scoring models based on crosslink data obtained from XL-MS 
Type Of Material Improvements to research infrastructure 
Year Produced 2015 
Provided To Others? Yes  
Impact The methods has been used by us an others in the EM community, also in via CCP-EM to validated models in cryoEM maps. Some of the publications describing the use of the software to validate different structures can be found here: http://tempy.ismb.lon.ac.uk/ 
URL http://tempy.ismb.lon.ac.uk/
 
Title HVint 
Description A database containing known and predicted interaction in herpes simplex virus type 1 (HSV-1) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Ashford et al 2015 (PMID: 27384951) 
URL http://topf-group.ismb.lon.ac.uk/hvint/
 
Description A hybrid approach to revealing interaction networks and intermediate structures of herpes viruses 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Country United Kingdom 
Sector Academic/University 
PI Contribution Our key goal is to study the interactions and structures of viron subcomplexes during herpesviruses infection cycle. Together with the Alber Lab in USC we have developed an efficient mathematical programming algorithm that simultaneously fits all component structures into a cryoEM density map of a complex at low resolutions (e.g. from tomography - data provided by Prof. Grunewald). The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Our method generates an assembly configuration in a few seconds, allowing the generation of an ensemble of candidate solutions that can be assessed by an independent scoring function. The method was recently published in Bioinformatics (Zhang et al. 2010) and was recommended and highlighted by the 'Faculty of 1000'. The work was also be presented at the ISMB conference. In addition, we further developed methods for modelling, fitting and refining models in the context of cryoEM maps. First, we developed a web-server for automated homology modelling of assembly components by alternative alignments and fitting into cryoEM maps of their assemblies. The web-server (based on which a paper was published this year in Bioinformatics - Rawi et al. 2010) provides an interactive approach to improving the selection of models based on the quality of their fit into the EM map and enables a large scale modelling (http://choyce.ismb.lon.ac.uk/). Second, we have developed a number of new scoring functions for density fitting, two of which are as good if not better than the currently used score in density fitting (cross correlation). Finally, to improve our flexible fitting program Flex-EM (http://topf-group.ismb.lon.ac.uk/flex-em/), we have developed a method for identifying rigid bodies in proteins structure (RIBFIND). Dr. Grunewald and myself have a joint PhD student who works on modelling of glycoproteins sub-complexes from sub-tomogram averaged maps. She has also developed a protein interaction database and network for HSV-1 (hvint: http://topf-group.ismb.lon.ac.uk/hvint/ ).
Collaborator Contribution Dr. Grunewald has pioneered the application of cryo-electron tomography to isolated pleomorphic viruses revealing their three-dimensional supramolecular organization. His work on the virions of Herpes simplex virus has provided us with new challenges for fitting atomic structures into low-resolution EM maps of large virus assemblies during infection. Prof. Alber's lab has developed a method an efficient mathematical programming algorithm that simultaneously fits all component structures into an assembly electron microscopy density map. The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Over the past year, the IC group has extended the proteomic techniques employed in the lab and tailored their use towards our goal of elucidating HSV1-host protein interactions. This data is important to be provided as constraint to our modelling of HSV1 proteins during infection using tomograms.
Impact This collaboration is multidisciplinary, involving computational biology, structural biology and cell biology. Zhang et al. (PMID: 20529915) Pandurangan and Topf (PMID: 22079400) Pandurangan and Topf (PMID: 22796953) Maurer et al, and Grunewald (PMID: 23850455 ) Pandurangan et al, and Topf (PMID: 26655474) Farabella et al, and Topf (PMID: 26306092) Zeev-Ben-Mordehai et al (PMID: 27035968) Ashford et al (PMID: 27384951) Joseph et al. (PMID:26988127) Joseph et al. (PMID: 28735107) Joseph et al. (PMID: 28552721)
Start Year 2009
 
Description A hybrid approach to revealing interaction networks and intermediate structures of herpes viruses 
Organisation Osaka University
Department Department of Biological Sciences
Country Japan 
Sector Academic/University 
PI Contribution Our key goal is to study the interactions and structures of viron subcomplexes during herpesviruses infection cycle. Together with the Alber Lab in USC we have developed an efficient mathematical programming algorithm that simultaneously fits all component structures into a cryoEM density map of a complex at low resolutions (e.g. from tomography - data provided by Prof. Grunewald). The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Our method generates an assembly configuration in a few seconds, allowing the generation of an ensemble of candidate solutions that can be assessed by an independent scoring function. The method was recently published in Bioinformatics (Zhang et al. 2010) and was recommended and highlighted by the 'Faculty of 1000'. The work was also be presented at the ISMB conference. In addition, we further developed methods for modelling, fitting and refining models in the context of cryoEM maps. First, we developed a web-server for automated homology modelling of assembly components by alternative alignments and fitting into cryoEM maps of their assemblies. The web-server (based on which a paper was published this year in Bioinformatics - Rawi et al. 2010) provides an interactive approach to improving the selection of models based on the quality of their fit into the EM map and enables a large scale modelling (http://choyce.ismb.lon.ac.uk/). Second, we have developed a number of new scoring functions for density fitting, two of which are as good if not better than the currently used score in density fitting (cross correlation). Finally, to improve our flexible fitting program Flex-EM (http://topf-group.ismb.lon.ac.uk/flex-em/), we have developed a method for identifying rigid bodies in proteins structure (RIBFIND). Dr. Grunewald and myself have a joint PhD student who works on modelling of glycoproteins sub-complexes from sub-tomogram averaged maps. She has also developed a protein interaction database and network for HSV-1 (hvint: http://topf-group.ismb.lon.ac.uk/hvint/ ).
Collaborator Contribution Dr. Grunewald has pioneered the application of cryo-electron tomography to isolated pleomorphic viruses revealing their three-dimensional supramolecular organization. His work on the virions of Herpes simplex virus has provided us with new challenges for fitting atomic structures into low-resolution EM maps of large virus assemblies during infection. Prof. Alber's lab has developed a method an efficient mathematical programming algorithm that simultaneously fits all component structures into an assembly electron microscopy density map. The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Over the past year, the IC group has extended the proteomic techniques employed in the lab and tailored their use towards our goal of elucidating HSV1-host protein interactions. This data is important to be provided as constraint to our modelling of HSV1 proteins during infection using tomograms.
Impact This collaboration is multidisciplinary, involving computational biology, structural biology and cell biology. Zhang et al. (PMID: 20529915) Pandurangan and Topf (PMID: 22079400) Pandurangan and Topf (PMID: 22796953) Maurer et al, and Grunewald (PMID: 23850455 ) Pandurangan et al, and Topf (PMID: 26655474) Farabella et al, and Topf (PMID: 26306092) Zeev-Ben-Mordehai et al (PMID: 27035968) Ashford et al (PMID: 27384951) Joseph et al. (PMID:26988127) Joseph et al. (PMID: 28735107) Joseph et al. (PMID: 28552721)
Start Year 2009
 
Description A hybrid approach to revealing interaction networks and intermediate structures of herpes viruses 
Organisation Princeton University
Country United States 
Sector Academic/University 
PI Contribution Our key goal is to study the interactions and structures of viron subcomplexes during herpesviruses infection cycle. Together with the Alber Lab in USC we have developed an efficient mathematical programming algorithm that simultaneously fits all component structures into a cryoEM density map of a complex at low resolutions (e.g. from tomography - data provided by Prof. Grunewald). The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Our method generates an assembly configuration in a few seconds, allowing the generation of an ensemble of candidate solutions that can be assessed by an independent scoring function. The method was recently published in Bioinformatics (Zhang et al. 2010) and was recommended and highlighted by the 'Faculty of 1000'. The work was also be presented at the ISMB conference. In addition, we further developed methods for modelling, fitting and refining models in the context of cryoEM maps. First, we developed a web-server for automated homology modelling of assembly components by alternative alignments and fitting into cryoEM maps of their assemblies. The web-server (based on which a paper was published this year in Bioinformatics - Rawi et al. 2010) provides an interactive approach to improving the selection of models based on the quality of their fit into the EM map and enables a large scale modelling (http://choyce.ismb.lon.ac.uk/). Second, we have developed a number of new scoring functions for density fitting, two of which are as good if not better than the currently used score in density fitting (cross correlation). Finally, to improve our flexible fitting program Flex-EM (http://topf-group.ismb.lon.ac.uk/flex-em/), we have developed a method for identifying rigid bodies in proteins structure (RIBFIND). Dr. Grunewald and myself have a joint PhD student who works on modelling of glycoproteins sub-complexes from sub-tomogram averaged maps. She has also developed a protein interaction database and network for HSV-1 (hvint: http://topf-group.ismb.lon.ac.uk/hvint/ ).
Collaborator Contribution Dr. Grunewald has pioneered the application of cryo-electron tomography to isolated pleomorphic viruses revealing their three-dimensional supramolecular organization. His work on the virions of Herpes simplex virus has provided us with new challenges for fitting atomic structures into low-resolution EM maps of large virus assemblies during infection. Prof. Alber's lab has developed a method an efficient mathematical programming algorithm that simultaneously fits all component structures into an assembly electron microscopy density map. The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Over the past year, the IC group has extended the proteomic techniques employed in the lab and tailored their use towards our goal of elucidating HSV1-host protein interactions. This data is important to be provided as constraint to our modelling of HSV1 proteins during infection using tomograms.
Impact This collaboration is multidisciplinary, involving computational biology, structural biology and cell biology. Zhang et al. (PMID: 20529915) Pandurangan and Topf (PMID: 22079400) Pandurangan and Topf (PMID: 22796953) Maurer et al, and Grunewald (PMID: 23850455 ) Pandurangan et al, and Topf (PMID: 26655474) Farabella et al, and Topf (PMID: 26306092) Zeev-Ben-Mordehai et al (PMID: 27035968) Ashford et al (PMID: 27384951) Joseph et al. (PMID:26988127) Joseph et al. (PMID: 28735107) Joseph et al. (PMID: 28552721)
Start Year 2009
 
Description A hybrid approach to revealing interaction networks and intermediate structures of herpes viruses 
Organisation University of Oxford
Department Division of Structural Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution Our key goal is to study the interactions and structures of viron subcomplexes during herpesviruses infection cycle. Together with the Alber Lab in USC we have developed an efficient mathematical programming algorithm that simultaneously fits all component structures into a cryoEM density map of a complex at low resolutions (e.g. from tomography - data provided by Prof. Grunewald). The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Our method generates an assembly configuration in a few seconds, allowing the generation of an ensemble of candidate solutions that can be assessed by an independent scoring function. The method was recently published in Bioinformatics (Zhang et al. 2010) and was recommended and highlighted by the 'Faculty of 1000'. The work was also be presented at the ISMB conference. In addition, we further developed methods for modelling, fitting and refining models in the context of cryoEM maps. First, we developed a web-server for automated homology modelling of assembly components by alternative alignments and fitting into cryoEM maps of their assemblies. The web-server (based on which a paper was published this year in Bioinformatics - Rawi et al. 2010) provides an interactive approach to improving the selection of models based on the quality of their fit into the EM map and enables a large scale modelling (http://choyce.ismb.lon.ac.uk/). Second, we have developed a number of new scoring functions for density fitting, two of which are as good if not better than the currently used score in density fitting (cross correlation). Finally, to improve our flexible fitting program Flex-EM (http://topf-group.ismb.lon.ac.uk/flex-em/), we have developed a method for identifying rigid bodies in proteins structure (RIBFIND). Dr. Grunewald and myself have a joint PhD student who works on modelling of glycoproteins sub-complexes from sub-tomogram averaged maps. She has also developed a protein interaction database and network for HSV-1 (hvint: http://topf-group.ismb.lon.ac.uk/hvint/ ).
Collaborator Contribution Dr. Grunewald has pioneered the application of cryo-electron tomography to isolated pleomorphic viruses revealing their three-dimensional supramolecular organization. His work on the virions of Herpes simplex virus has provided us with new challenges for fitting atomic structures into low-resolution EM maps of large virus assemblies during infection. Prof. Alber's lab has developed a method an efficient mathematical programming algorithm that simultaneously fits all component structures into an assembly electron microscopy density map. The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. Over the past year, the IC group has extended the proteomic techniques employed in the lab and tailored their use towards our goal of elucidating HSV1-host protein interactions. This data is important to be provided as constraint to our modelling of HSV1 proteins during infection using tomograms.
Impact This collaboration is multidisciplinary, involving computational biology, structural biology and cell biology. Zhang et al. (PMID: 20529915) Pandurangan and Topf (PMID: 22079400) Pandurangan and Topf (PMID: 22796953) Maurer et al, and Grunewald (PMID: 23850455 ) Pandurangan et al, and Topf (PMID: 26655474) Farabella et al, and Topf (PMID: 26306092) Zeev-Ben-Mordehai et al (PMID: 27035968) Ashford et al (PMID: 27384951) Joseph et al. (PMID:26988127) Joseph et al. (PMID: 28735107) Joseph et al. (PMID: 28552721)
Start Year 2009
 
Description ATP-triggered molecular mechanics of the chaperonin GroEL 
Organisation Birkbeck, University of London
Department Department of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the association of the co-chaperonin GroES, followed by further large movements that eject the substrate polypeptide from a ring of hydrophobic binding sites into a GroES-capped, hydrophilic folding chamber. In collaboration with Prof. Helen Saibil, Birkbeck College, we used data from cryo-electron microscopy (EM) to resolve a set of distinct GroEL-ATP conformations that can be ordered into a trajectory of domain rotation and elevation. For that, we used our flexible fitting program Flex-EM. Based on our refinement we found that the initial conformations are likely to be the ones that capture polypeptide substrate. Then the binding domains extend radially to separate from each other, but maintain their binding surfaces facing the cavity, potentially exerting mechanical force upon kinetically trapped, misfolded substrates. The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the "power stroke" that ejects substrate into the folding chamber.
Collaborator Contribution The group of Helen Saibil performed the experiments for this work as well as image processing. We currently have a joint PhD student looking at various GroEL maps at multiple resolution to compare the different conformations.
Impact Clare DK et al. 2012 (PMID: 22445172); Joseph et al, 2017 (PMID: 28552721)
Start Year 2010
 
Description Collaboration with CCP-EM 
Organisation Daresbury Laboratory
Country United Kingdom 
Sector Private 
PI Contribution We collaborate on the CCP-EM (Collaborative Computational Project for Electron cryo-Microscopy) project. This project is supported by MRC. We implement some of the software developed in my group via the CCP-EM platform. The idea is to support the users of software for cryo-EM through dissemination of information on available software, and directed training.
Collaborator Contribution Our collaborators (under the supervision of Dr. Martyn Winn) are in the process of making our Flex-EM/RIBFIND software as well as TEMPy available via CCP-EM.
Impact We had a number of productive meetings and workshops. We are working on a number of software packages developed in my group to be implemented in CCP-EM (Flex-EM, RIBFIND, TEMPy). publications: Wood et al. (2015) PMID: 25615866 Joseph et al (2016) PMID: 26988127 Joseph et al (2017) PMID: 28552721 We received a joint MRC Partnership grant together with Martyn Winn (PI) and other 9 Co-Is across the UK. (MR/N009614/1)
Start Year 2012
 
Description Modelling microtubule with microtubule binding proteins 
Organisation Birkbeck, University of London
Department Department of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been generating atomic models of microtubule complexes using 3D cryoEM density maps.
Collaborator Contribution Professor Carolyn Moores studies microtubule organisation and dynamics using cryo electron microscopy methods.
Impact Atherton et al 2014 (PMID: 25209998) Atherton et al 2017 (PMID: 28826477) Atherton et al 2017 (PMID: 28991265) Locke et al 2018 (PMID: 29078367)
Start Year 2014
 
Title Jwalk 
Description The software helps in the calculation of solvent accessible surface distance between cross-linked residues. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact We show that using our methods we can perform accurate calculations of the SASD and use it for accurate scoring of models using cross-linking mass-spectrometry data. Paper: Bullock et al ( PMID: 27150526 ) 
URL http://topf-group.ismb.lon.ac.uk/Software.html
 
Description CCP-EM Developers Meeting 2016 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact CCP-EM Developers Meeting
Year(s) Of Engagement Activity 2016
 
Description EMBO course on integrative modelling of biomolecular interactions 
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 EMBO course on integrative modelling of biomolecular interactions
Year(s) Of Engagement Activity 2016
URL http://events.embo.org/16-biomol-interact/
 
Description EMBO practical course on cryoEM and image processing 
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 EMBO practical course on cryoEM and image processing
Year(s) Of Engagement Activity 2016
URL https://www.embl.de/training/events/2016/CRY16-01/
 
Description public talk in Birkbeck Science week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact general talk about the role of computational modelling in Structural Biology
Year(s) Of Engagement Activity 2016
URL http://www.bbk.ac.uk/science/about-us/events/science-week/science-week-2016-highlights