Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

2024-02-01 Thread Frank von Delft 

That's great news!

On 01/02/2024 10:34, Deborah Harrus wrote:


Dear Frank,

We are indeed harvesting restraints used in refinement, but not 
distributing them yet. This should come later this year or early 2025, 
and can be made retrospectively.


Kind regards,

Deborah

On 31/01/2024 14:15, Frank von Delft wrote:

Hi Deborah - sounds great, well done!

Are you yet harvesting and serving up the restraints used in 
refinement?  If not, that remains a huge gap, in my view.  (The 
chemists tend not to be aware that's even a thing, I keep discovering.)


Frank


On 31/01/2024 13:57, Deborah Harrus wrote:


*Dear all,*

*We're excited to announce significant improvements to ligand data 
access and organisation within the PDBe FTP area. These updates aim 
to empower your research by simplifying data retrieval and providing 
deeper insights into protein-ligand interactions.*


*Key Enhancements:*

 *

*Comprehensive Ligand Interaction Data: Two new data files,
Interacting_chains_with_ligand_functions.tsv and
pdb_bound_molecules.tsv, enable large-scale analyses of ligand
interactions across the entire PDB archive including functional
categorisation such as drug-like, reactant-like or cofactor-like.*

 *

*Streamlined FTP Directory Structure: The revamped FTP area
features dedicated folders for Chemical Component Definitions
(CCDs), Peptide-like Reference Definitions (PRDs), Covalently
Linked Components (CLCs), and additional data files,
facilitating intuitive data navigation.*

*Benefits for You:*

 *

*Perform large-scale ligand interaction analyses across the
entire PDB using complete ligand representations.*

 *

*Quick access to all the ligands bound to a specific protein or
identifying all the proteins binding to a specific ligand*

 *

*Gain deeper insights into protein function through ligand
interaction and classification.*

 *

*Easily access and navigate ligand data with clear file
organisation and unique identifiers.*

*We believe these improvements will enhance ligand data analysis 
through streamlined data access and additional functional insights. *


*For more information, visit the PDBe news item 
at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp 
*


*Or visit the PDBe FTP area 
directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ 
*


*Should you have any questions or require further assistance, please 
don't hesitate to contact us.*


*

Sincerely,

Deborah Harrus

The PDBe Team

*
--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---





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Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

2024-02-01 Thread Deborah Harrus 

Dear Frank,

We are indeed harvesting restraints used in refinement, but not 
distributing them yet. This should come later this year or early 2025, 
and can be made retrospectively.


Kind regards,

Deborah

On 31/01/2024 14:15, Frank von Delft wrote:

Hi Deborah - sounds great, well done!

Are you yet harvesting and serving up the restraints used in 
refinement?  If not, that remains a huge gap, in my view.  (The 
chemists tend not to be aware that's even a thing, I keep discovering.)


Frank


On 31/01/2024 13:57, Deborah Harrus wrote:


*Dear all,*

*We're excited to announce significant improvements to ligand data 
access and organisation within the PDBe FTP area. These updates aim 
to empower your research by simplifying data retrieval and providing 
deeper insights into protein-ligand interactions.*


*Key Enhancements:*

 *

*Comprehensive Ligand Interaction Data: Two new data files,
Interacting_chains_with_ligand_functions.tsv and
pdb_bound_molecules.tsv, enable large-scale analyses of ligand
interactions across the entire PDB archive including functional
categorisation such as drug-like, reactant-like or cofactor-like.*

 *

*Streamlined FTP Directory Structure: The revamped FTP area
features dedicated folders for Chemical Component Definitions
(CCDs), Peptide-like Reference Definitions (PRDs), Covalently
Linked Components (CLCs), and additional data files, facilitating
intuitive data navigation.*

*Benefits for You:*

 *

*Perform large-scale ligand interaction analyses across the
entire PDB using complete ligand representations.*

 *

*Quick access to all the ligands bound to a specific protein or
identifying all the proteins binding to a specific ligand*

 *

*Gain deeper insights into protein function through ligand
interaction and classification.*

 *

*Easily access and navigate ligand data with clear file
organisation and unique identifiers.*

*We believe these improvements will enhance ligand data analysis 
through streamlined data access and additional functional insights. *


*For more information, visit the PDBe news item 
at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp 
*


*Or visit the PDBe FTP area 
directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ 
*


*Should you have any questions or require further assistance, please 
don't hesitate to contact us.*


*

Sincerely,

Deborah Harrus

The PDBe Team

*
--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 






--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

2024-01-31 Thread Frank von Delft 

Hi Deborah - sounds great, well done!

Are you yet harvesting and serving up the restraints used in 
refinement?  If not, that remains a huge gap, in my view.  (The chemists 
tend not to be aware that's even a thing, I keep discovering.)


Frank


On 31/01/2024 13:57, Deborah Harrus wrote:


*Dear all,*

*We're excited to announce significant improvements to ligand data 
access and organisation within the PDBe FTP area. These updates aim to 
empower your research by simplifying data retrieval and providing 
deeper insights into protein-ligand interactions.*


*Key Enhancements:*

 *

*Comprehensive Ligand Interaction Data: Two new data files,
Interacting_chains_with_ligand_functions.tsv and
pdb_bound_molecules.tsv, enable large-scale analyses of ligand
interactions across the entire PDB archive including functional
categorisation such as drug-like, reactant-like or cofactor-like.*

 *

*Streamlined FTP Directory Structure: The revamped FTP area
features dedicated folders for Chemical Component Definitions
(CCDs), Peptide-like Reference Definitions (PRDs), Covalently
Linked Components (CLCs), and additional data files, facilitating
intuitive data navigation.*

*Benefits for You:*

 *

*Perform large-scale ligand interaction analyses across the entire
PDB using complete ligand representations.*

 *

*Quick access to all the ligands bound to a specific protein or
identifying all the proteins binding to a specific ligand*

 *

*Gain deeper insights into protein function through ligand
interaction and classification.*

 *

*Easily access and navigate ligand data with clear file
organisation and unique identifiers.*

*We believe these improvements will enhance ligand data analysis 
through streamlined data access and additional functional insights. *


*For more information, visit the PDBe news item 
at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp 
*


*Or visit the PDBe FTP area 
directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ 
*


*Should you have any questions or require further assistance, please 
don't hesitate to contact us.*


*

Sincerely,

Deborah Harrus

The PDBe Team

*
--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 








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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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