User: Vladimir Chupakhin

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520
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Location:
Toledo, Spain
Website:
http://farmacokratia.b...
Last seen:
4 years, 8 months ago
Joined:
9 years, 4 months ago
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Mining life science data

Posts by Vladimir Chupakhin

<prev • 83 results • page 2 of 9 • next >
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Comment: C: Protein Superfamily Annotation
... yep, seems good: interpro_id -- interpro_description -- uniprot_ac ...
written 6.7 years ago by Vladimir Chupakhin520
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Protein Superfamily Annotation
... Hello! can you please suggest me the database with annotation for "classical" superfamilies like GPCR A, GPCR B, GPCR C, Ion channels, Ligand-gated ion channel, Nuclear receptors, etc. That's easy to do with the EC, but of course it does not include the above mentioned examples. Thank's in advance! ...
annotation protein written 6.7 years ago by Vladimir Chupakhin520 • updated 6.7 years ago by David Westergaard1.4k
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Comment: C: Annotate Uniprotac With Taxonomic Lineage
... Yes, I did that way. But I was looking for "online" solution, so I can check on the flight, esp. when the UNIPROT is updated regularly...thus I need update the list, also regularly. ...
written 6.8 years ago by Vladimir Chupakhin520
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Comment: C: Annotate Uniprotac With Taxonomic Lineage
... I was looking for other solutions, parsing txt/xml will take a lot of time. I am currently using only mammals list - that can help, but it need an update. ...
written 6.8 years ago by Vladimir Chupakhin520
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Comment: C: Annotate Uniprotac With Taxonomic Lineage
... on the uniprot page there is a info: Taxonomic lineage Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo I want to download that data... ...
written 6.8 years ago by Vladimir Chupakhin520
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Annotate Uniprotac With Taxonomic Lineage
... Hello! I need your advice on how to annotate the protein (uniprotAC) with taxonomy lineage. http://www.uniprot.org/uniprot/?query=$(QueryProperty)&format=tab&columns=$(columns) where columns are id,genes,domains,ec,database(PDB),organism,organism-id Actually I got lost on the step t ...
uniprot written 6.8 years ago by Vladimir Chupakhin520 • updated 5.2 years ago by txino0
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Answer: A: How To Decide Best Docking Conformation From Autodock Results?
... For detecting the best docked conformation 1. look for the best 2. use interaction fingerprint for compound known to be active at this target and that do have experimentally derived protein-ligand complex http://www.slideshare.net/chupvl/interaction-fingerprint-1d-encoding-of-3d-proteinligand-info ...
written 6.9 years ago by Vladimir Chupakhin520
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Answer: A: How To Obtain True Positive And True Negative Datasets To Be Used In Training A
... Most common method is to use DUD or newer version - DUDe. The generated compounds - called decoys, active compounds can be found in ChEMBL. ...
written 7.0 years ago by Vladimir Chupakhin520
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Answer: A: C++ Api To Mutate Pdb Residues
... OpenEye OEChemTK - commercial, but open to the academic ...
written 7.2 years ago by Vladimir Chupakhin520
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Answer: A: Insilico Mutation Analysis For Amino Acid Residues
... There are many tools, take a look for example at I-Mutant 2.0.6 – A Tool for Predicting Protein Stability upon Mutation CUPSAT – Protein Stability Analysis Tool SNAP – Predicts Effect of Mutations on Protein Function iStable: off-the-shelf predictor integration for predicting protein stability cha ...
written 7.2 years ago by Vladimir Chupakhin520

Latest awards to Vladimir Chupakhin

Popular Question 5.7 years ago, created a question with more than 1,000 views. For Protein Functional Classes
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Implementation Of Π-Π And Aromatic Interactions In Protein-Ligand Interactions
Scholar 6.0 years ago, created an answer that has been accepted. For A: How To Obtain True Positive And True Negative Datasets To Be Used In Training A
Supporter 6.2 years ago, voted at least 25 times.
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Implementation Of Π-Π And Aromatic Interactions In Protein-Ligand Interactions
Teacher 8.3 years ago, created an answer with at least 3 up-votes. For A: List Of Organization That Are Looking For Freelancer Bioinformatics, Genetics Or
Teacher 8.5 years ago, created an answer with at least 3 up-votes. For A: Protein Small Molecular Docking

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