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faq [2015/09/17 15:27] – [How to I access PDB files for CATH domains?] hafsafaq [2023/09/28 14:01] (current) – vwaman
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 === Core CATH Team === === Core CATH Team ===
  
-[[cathteam:cuff | Alison Cuff]]  is the present CATH Curator and Manager; [[cathteam:sillitoe | Ian Sillitoe]] is the present CATH Technical Manager.  [[cathteam:lewis | Tony Lewis ]] was a Research Assistant in the group and was heavily involved in the development of the new CATH update protocol as part of CATH v3.0. He is still involved in maintaining and updating CATH in an ongoing consultancy capacity. [[cathteam:clegg | Andrew Clegg]] is developing web services for CATH.+[[cathteam:sillitoe | Ian Sillitoe]] is the CATH Manager.  [[cathteam:bordin | Nicola Bordin ]] is a Research Associate  and is involved in algorithms development for the generation of Functional Families and their applications. [[cathteam:dawson | Natalie Dawson]] was the CATH curator and a Research Associate in the group. [[cathteam:waman | Vaishali Waman ]] is a Research Associate in the team and she is now the CATH curator.
  
  
  
-===== FAQ: Cath Data =====+===== FAQ: CATH Data =====
  
 ==== What do the letters "C.A.T.H.S.O.L.I.D" mean? ==== ==== What do the letters "C.A.T.H.S.O.L.I.D" mean? ====
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 This was due to the wwPDB remediation project. Please click [[http://remediation.wwpdb.org/ | here]] for further information.  This was due to the wwPDB remediation project. Please click [[http://remediation.wwpdb.org/ | here]] for further information. 
 +
 +==== Why did FunFam identifiers change between v4.2.0 and v4.3.0? ====
 +
 +FunFams now have a more consistent numbering scheme based on the amount of sequences contained in the 'seed' alignments at their time of generation. FunFam 1 has the highest number or sequences, FF2 the second-highest, and so on.
  
 ===== FAQ: Web Pages ===== ===== FAQ: Web Pages =====
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 The answer to this is use the CATH webservices. However, the CATH webservices are undergoing a major revamp and are still in testing. We will update this section when we move the webservices to production.  The answer to this is use the CATH webservices. However, the CATH webservices are undergoing a major revamp and are still in testing. We will update this section when we move the webservices to production. 
  
-==== How do I link to the CATH database from my resource? ====+==== How do I get a link to my resource from the CATH database? ====
  
-We have moved to using clearer accession URLs for entities in CATH that generally follow the form: +If you would like us to link to your resource and there is a natural mapping from one of the CATH entities (PDB, PDB Chain, Domain, Classification, etc) then [[http://www.cathdb.info/support/contact|get in touch]].
- +
-  http://{VERSION}.cathdb.info/{ENTITY}/{ID} +
- +
-The following table provides a brief overview of the possible accessors for each CATH entity and is intended as a placeholder until a more complete discussion is added. +
- +
- +
-^ ENTITY ^ Path ^ Example ^ +
-| Domain | /domain/{ID} | http://www.cathdb.info/domain/1cukA01 | +
-| Chain  | /chain/{ID}  | http://www.cathdb.info/chain/1cukA | +
-| Pdb    | /pdb/{ID}    | http://www.cathdb.info/pdb/1cuk | +
-| Classification | /cathnode/{ID} | http://www.cathdb.info/cathnode/1.10.10.10 | +
- +
-We are working towards making these revised URLs compatible with previous versions of CATH. However, due to the significant changes between CATH v3.1 and v3.2, this isn't a particularly trivial job so please bear with us. +
- +
-^ VERSION  ^ Example  ^ +
-| v3-1  | http://v3-1.cathdb.info  | +
-| v3-2  | http://v3-2.cathdb.info  | +
- +
- +
-==== How to I access PDB files for CATH domains? ==== +
- +
-The following links provide PDB coordinates for the PDB (1cuk), PDB Chain (1cukA) and CATH domain (1cukA01): +
- +
-http://www.cathdb.info/search/by_text?q=1cuk +
-http://www.cathdb.info/chain/1cukA +
-http://www.cathdb.info/version/latest/domain/1cukA01 +
- +
-==== How do I get a link to my resource from the CATH database? ====+
  
-If you would like us to link to your resource and there is a natural mapping from one of the CATH entities (PDB, PDB Chain, Domain, Classification, etc) then [[contact|get in touch]].+==== Which is the latest version of the CATH? ==== 
 +CATH v4.3 is the latest CATH release. Please find more details in below paper: 
 +Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CSM, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021 Jan 8;49(D1):D266-D273. doi: 10.1093/nar/gkaa1079.  
  
faq.1442503636.txt.gz · Last modified: by hafsa

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