CCP4
CCP4
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Analysing models from ultra-high resolution crystallography - Ashwin Chari
Modern methods in Structural Biology aim to provide detailed insights into how proteins are able to catalyse and control chemical reactions. In addition, the conformational dynamics of proteins are being intensively studied with regards to their role in the regulation of enzyme catalysis, for example by allosteric phenomena. In recent years, time-resolved (TR) X-ray crystallography and structural enzymology have been revived by the advent of serial crystallography at advanced X-ray sources and by new methods for sample delivery, reaction initiation and data processing, making TR studies increasingly accessible. However, electron density maps resulting from TR studies typically correspond to mixtures of states, thus their interpretation thus presents a serious challenge. We are addressing this challenge by supplementing TR structural data with ultra-high-resolution data from macrocrystals of highly homogenous mechanistically trapped states. Routinely achieving ultra-high resolution requires optimised sample quality, top-hat beams of adjustable size and shape, data collection with high-energy X-rays and CdTe detectors, using optimal data strategies designed and executed through direct control by a Workflow. In this talk, I will present
some of our recent work, highlighting what is now possible for Structural Enzymology using X-ray crystallography, yet currently inaccessible by cryo-EM and Artificial Intelligence methods. I will also highlight some of the challenges faced in the pursuit of accurate models to explain ultra-high resolution diffraction data.
Переглядів: 71

Відео

Probing crystallin using serial UV/X-ray crystallography - Briony Yorke
Переглядів 311Місяць тому
Serial crystallography provides opportunities to investigate protein dynamics at high spatial and temporal resolution. We are applying this technique to the investigation of photostability and photodamage to proteins to identify conformational changes that occur in response to exposure to light. Ultraviolet radiation (UVR) is known to induce structural changes in proteins through two major path...
Teasing out the secrets of subtle protein dynamics - Helen Ginn
Переглядів 138Місяць тому
Structural biology experiments are focusing increasingly with the small, subtle motions underpinning protein function. Our collective understanding of how these subtle motions translate to functional impact is limited, and this is hampering efforts in protein engineering and drug development. The Protein Machinists’ lab develops conceptual frameworks for defining, modelling and navigating the p...
Validation of Ligands: Making decisions while modelling - Oliver Smart
Переглядів 144Місяць тому
The production of an X-ray crystal structure for a protein-ligand complex involves many steps, encompassing experimental and computational crystallography as well as chemoinformatics and computational chemistry. Using examples taken from the PDB, we show how a mistake made in any of these steps adversely affects the quality of the resulting structure, including that of the ligand. Validation pr...
Managing your data with LIMS systems - Ed Daniel
Переглядів 80Місяць тому
Automation and other high-throughput techniques have greatly increased the amount of data generated by MX experiments [1]. There is a commensurate need for research data management tools to ensure a complete chain of custody from protein sequence through to structure deposition. We discuss the benefits and risks inherent in Laboratory Information Management Systems (LIMS). We cover this in gene...
Decision making in MX - how to be a productive structural biologist - Judit Debreczeni
Переглядів 161Місяць тому
Structure determination of macromolecules is undoubtedly a complex process, with multiple decision making points along every step. Although many of these have gone through extensive automation over the last decade, almost entirely removing the need for human intervention in straight-forward or precedented cases, decisions still need to be made when automated solutions prove insufficient. In the...
Everything, Everywhere, All at Once: multi-state, multi-dataset, multi-model refinement -Nick Pearce
Переглядів 97Місяць тому
The process of building and refining accurate macromolecular models remains critical for obtaining high-resolution structural information. Traditional refinement approaches often still involve the time-consuming optimization of a single model against a single experimental data set. However, with increasing automation, especially in the study of weak structural features such as ligand binding in...
Xtrapol8: Identifying and modelling low-occupancy states in MX crystallography - Elke De Zitter
Переглядів 88Місяць тому
Xtrapol8 is a program that aims to aid structural biologists in identifying and modeling low occupancy states in macromolecular crystallography.1 It was originally written for the analysis of time-resolved crystallography data, to compare electron density maps and structures acquired before and after the application of a trigger. Nevertheless, Xtrapol8 can also be applied to other cases in whic...
Same but different: serial data collection and processing - Arwen Pearson
Переглядів 324Місяць тому
The data collection and processing of macromolecular single crystal rotation data is well established at synchrotrons and lab sources world-wide with automated pipelines competitive with expert users in terms of data quality. Serial data are a different kettle of fish. I will introduce some of the different flavours of serial and multi-crystal data collection methods and approaches that can be ...
Dealing with metal containing ligands - Garib Murshudov
Переглядів 119Місяць тому
Over the last two decades the quality of internal structures of ligands in the PDB has been improved substantially. The main reason for such improvements is the huge efforts put in by the wwPDB. Apart from the PDB, software tools associated with the refinement programs have also been developed and improved. Developments of such software tools as GRADE/GRADE21, phenix.elbow2 and AceDRG3 has help...
Building atomic models of glycans with confidence - Lucy Schofield
Переглядів 707Місяць тому
The introduction of intuitive graphical interfaces has enabled structural biologists who are not crystallographers to build complete protein or nucleic acid models automatically. Up until recently, carbohydrates were in a different league, with very little automation available. While ongoing efforts to address legacy issues, such as incorrect dictionaries or non-standard atom naming, have impro...
Seven years of ISOLDE: Lessons learned and paths forward - Tristan Croll
Переглядів 255Місяць тому
Starting with its first beta release in 2018, ISOLDE has been designed explicitly to ease the challenges unique to working with less-than-ideal crystallographic or cryo-EM data, in the regime where density combined with traditional bonded restraints are insufficient for reliable model building (i.e. resolutions below about 2-2.5 Å. The more complete physical representation provided by molecular...
Being Efficient (or Lazy) in Coot - Paul Emsley
Переглядів 142Місяць тому
The interactive model-building software Coot is often used in the x-ray crystallography structure solution process. Over the last six years it has undergone some major changes, including in October, the release of version 1.1. This version of Coot has • a more modern interface, largely following the "one window" paradigm, • interactive navigation and validation during Real Space Refinement, • u...
Key note: Lessons learned from SARS-CoV2 drug screening campaigns - Patrick Reinke
Переглядів 285Місяць тому
The Covid-19 pandemic has led to some major collaborations in which large-scale projects were organized. One of these was the SARS-CoV-2 task force at DESY, which involved more than 100 scientists from all over the world. An X-ray crystallographic screening of the SARS-CoV-2 main protease was carried out, in which 5953 compounds from two repurposing libraries were tested. Within one month, almo...
Use the right tool, right: making the best use of the right X-ray facility for your science G Winter
Переглядів 172Місяць тому
Over the last decade or so there have been substantial changes in the landscape around biological crystallography: the arrival of X-ray free electron lasers, the appearance of alpha fold, the coming of age of time resolved crystallography and the development of high throughput techniques enabling large fragment screening campaigns. This has created a land of opportunity for the structural biolo...
AlphaFold and it’s impact on streamlining structure solution - Dorothee Liebschner
Переглядів 363Місяць тому
AlphaFold and it’s impact on streamlining structure solution - Dorothee Liebschner
Identifying radiation damage and avoiding it in the first place - Elspeth Garman
Переглядів 136Місяць тому
Identifying radiation damage and avoiding it in the first place - Elspeth Garman
Round table discussion - Crystallography is dead! Long Live Crystallography!
Переглядів 166Місяць тому
Round table discussion - Crystallography is dead! Long Live Crystallography!
Automated workflows for strategy computation & data collection at synchrotron beamlines -Rasmus Fogh
Переглядів 212Місяць тому
Automated workflows for strategy computation & data collection at synchrotron beamlines -Rasmus Fogh
Light atoms identification and location by anomalous scattering - Kamel El Omari
Переглядів 83Місяць тому
Light atoms identification and location by anomalous scattering - Kamel El Omari
Dealing with Aperiodic Protein Crystal Structures - Gloria Borghasti
Переглядів 712 місяці тому
Dealing with Aperiodic Protein Crystal Structures - Gloria Borghasti
State of the art scaling and merging - Kevin Dalton
Переглядів 722 місяці тому
State of the art scaling and merging - Kevin Dalton
The data behind the cryo-EM structure, the microscope behind the data. - Kyle Morris
Переглядів 562 місяці тому
The data behind the cryo-EM structure, the microscope behind the data. - Kyle Morris
Things you don’t want to see in your data - and what could be done. - Andrey Lebedev
Переглядів 842 місяці тому
Things you don’t want to see in your data - and what could be done. - Andrey Lebedev
Robust statistics for serial crystallography data processing - Marjan Hadian Jazi
Переглядів 702 місяці тому
Robust statistics for serial crystallography data processing - Marjan Hadian Jazi
Observing dynamics in proteins from diffuse scattering - Steve Meisburger INCOMPLETE
Переглядів 732 місяці тому
Observing dynamics in proteins from diffuse scattering - Steve Meisburger INCOMPLETE
ExaFEL - exascale computing for SFX data processing - Derek Mendez
Переглядів 1902 місяці тому
ExaFEL - exascale computing for SFX data processing - Derek Mendez
Be prepared. Good data from good sample preparation - Maria Garcia Alai
Переглядів 792 місяці тому
Be prepared. Good data from good sample preparation - Maria Garcia Alai
Microbial and Antimicrobial Amyloids in Infections and Neurodegeneration - Meytal Landau
Переглядів 802 місяці тому
Microbial and Antimicrobial Amyloids in Infections and Neurodegeneration - Meytal Landau
An educational introduction to the statistics we use to judge and compare data sets - Greta M Assman
Переглядів 412 місяці тому
An educational introduction to the statistics we use to judge and compare data sets - Greta M Assman

КОМЕНТАРІ

  • @26d8
    @26d8 Місяць тому

    no sound?

  • @chandanvishwakarma8063
    @chandanvishwakarma8063 2 місяці тому

    interesting talk

  • @philippebenas5721
    @philippebenas5721 2 місяці тому

    Nice work as usual. Congrats Tassos, Robbie and all the team.

  • @jeffreyohren6624
    @jeffreyohren6624 2 місяці тому

    When you have a chance, would you please correct Dr. Borgstahl’s name in the title.

  • @murpholinox
    @murpholinox 10 місяців тому

    Very nice talk!

  • @ShivanshGupta6
    @ShivanshGupta6 Рік тому

    Can you please add writing with audio n videos..

  • @patricial1231
    @patricial1231 Рік тому

    1. Download the .sdf from the PDB for the small molecule 2. Open acedrg in CCP4 -> Change file type to .sdf -> input the .sdf file and add the three letter ID 3. Import the AcedrgOut.cif file into Coot. Add the ligand. Merge the Ligand. 4. In Coot go to Extensions -> Modules -> CCP4 -> Make link via AceDrg -> Click the 2 atoms to make the covalent bond

  • @equinema8673
    @equinema8673 2 роки тому

    very nice presentation! Thank you very much

  • @svenjabenn4879
    @svenjabenn4879 2 роки тому

    ☝️ þrðmð§m

  • @nathanwright1787
    @nathanwright1787 2 роки тому

    I hope you are well Melanie. X

  • @jianweimiao1602
    @jianweimiao1602 6 років тому

    Great job!