User: Jan Kosinski

gravatar for Jan Kosinski
Jan Kosinski1.6k
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Posts by Jan Kosinski

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Job: Postdoctoral position in integrated structural and systems biology
... I am looking for a highly talented postdoctoral researcher to join my newly established group at EMBL Hamburg and the Centre for Structural Systems Biology (CSSB). The group investigates infection cycles and host-pathogen interactions using computational and experimental approaches. The successful ...
modeling structural biology job system biology written 2.4 years ago by Jan Kosinski1.6k
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Comment: C: Calculate Distance Between Two Superposed Equivalent Atoms
... I think both 'superposed" and 'superimposed' is correct... ...
written 7.5 years ago by Jan Kosinski1.6k
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Comment: C: Calculate Distance Between Two Superposed Equivalent Atoms
... You'd better ask at modeller_usage mailing list: http://salilab.org/mailman/listinfo/modeller_usage . ...
written 7.5 years ago by Jan Kosinski1.6k
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Comment: C: Measuring Conservation
... Yes yes, sorry, I just wanted to say that your statement could be wrongly interpreted as that proteins DO NOT "maintain traceable some features related with their evolutionary origin" contrary to the nucleotide sequences, which is of course not true ;-) ...
written 7.5 years ago by Jan Kosinski1.6k
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Comment: C: Measuring Conservation
... I don't think that saying "Analyzing protein conservation you are mainly focused to functional constraints while nucleotide sequences maintain traceable some features related with their evolutionary origin" is true... Both protein and nucleotide sequences are used for studying evolutionary origins o ...
written 7.5 years ago by Jan Kosinski1.6k
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Comment: C: Is There Any Software/Server Which Can Give Missing Residues Of Pdb Files?
... The post from that modeller_usage mail list uses outdated modeller interface. Besides adding missing residues to PDB structures by modeling (de novo) make sense only in some applications. If 'true' phi/psi angles from PDB are needed, for example for statistical analysis, modeling by Modeller does no ...
written 7.5 years ago by Jan Kosinski1.6k
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Answer: A: Is There Any Software/Server Which Can Give Missing Residues Of Pdb Files?
... If PDB structure has a missing residue you just don't calculate phi/psi angles for neighboring residues... In a case you want to derive some statistics about phi & psi angles in protein structures, one direct solution to your problem is to use high resolution structures only. Such structures sho ...
written 7.5 years ago by Jan Kosinski1.6k
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Is There An Up To Date Database Of Catalytic Sites In Pdb Structures?
... Do you know a database of catalytic sites in PDB structures that is more or less up to date? According to the web page, Catalytic Site Atlas has been updated last time on 20th January 2010... ...
database written 7.5 years ago by Jan Kosinski1.6k
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Answer: A: Is It Good To Do Phylogeny Of Below Data
... No, it is not good data for phylogeny. Two most apparent reasons: You have selected all hydrolases, many can be completely dissimilar at the sequence level, thus precluding any reliable phylogeny based on sequences even if all hydrolases were similar at the sequence level, by selecting hydrolases ...
written 7.5 years ago by Jan Kosinski1.6k
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Comment: C: N-Gram Plots Using Pmc Or Pubmed Abstracts
... This may be due to i) wrong publication date assigned to some google books entries ii) default smoothing of the graph. This is the case for a "peak" of 'bioinformatics' term use around year 1900 :-) ...
written 7.6 years ago by Jan Kosinski1.6k

Latest awards to Jan Kosinski

Appreciated 7.4 years ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: How To Pronounce "De Bruijn"?
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: By What Criterion Can We Screen The Blast Results?
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: Webserver Applications And E-Mail Delivery Of Results
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: What Tool To Use For Protein-Rna Docking?
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.?
Appreciated 7.4 years ago, created a post with more than 5 votes. For Which Downloadable Database Of Pdb Ligand Binding Sites Would You Recommend?
Great Question 7.4 years ago, created a question with more than 5,000 views. For How Log-Odds Scores For Amino Acid Substitutions Matrices Should Be Calculated?
Good Question 7.4 years ago, asked a question that was upvoted at least 5 times. For How Log-Odds Scores For Amino Acid Substitutions Matrices Should Be Calculated?
Good Question 7.4 years ago, asked a question that was upvoted at least 5 times. For Which Downloadable Database Of Pdb Ligand Binding Sites Would You Recommend?
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: Conferences On Bioinformatics
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: How To Pronounce "De Bruijn"?
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: By What Criterion Can We Screen The Blast Results?
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: What Tool To Use For Protein-Rna Docking?
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.?
Popular Question 7.4 years ago, created a question with more than 1,000 views. For How Log-Odds Scores For Amino Acid Substitutions Matrices Should Be Calculated?
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Which Downloadable Database Of Pdb Ligand Binding Sites Would You Recommend?
Guru 7.4 years ago, received more than 100 upvotes.
Centurion 7.4 years ago, created 100 posts.
Voter 7.4 years ago, voted more than 100 times.
Supporter 7.4 years ago, voted at least 25 times.
Commentator 7.4 years ago, created a comment with at least 3 up-votes. For C: Beginner Book For Bioinformatics (Preferably In Python)
Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: Surface Amino-Acid From Sequence Only

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