User:Wayne Decatur/Structure analysis tools: Difference between revisions

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* [[FirstGlance_in_Jmol | FirstGlance in Jmol]] offers a detailed report on the numbers and properties of parts of chains not observed in a structure. Open your favorite molecule in FirstGlance in Jmol and then click on the 'Missing Residues' link on the first page that opens, under `Asymmetric Unit` section.
* [[FirstGlance_in_Jmol | FirstGlance in Jmol]] offers a detailed report on the numbers and properties of parts of chains not observed in a structure. Open your favorite molecule in FirstGlance in Jmol and then click on the 'Missing Residues' link on the first page that opens, under `Asymmetric Unit` section.
* Biopython can use REMARK 465 lines to parse missing residues, see my notebook `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo] ( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]). Also see [https://github.com/biopython/biopython/pull/1237 here] and [https://github.com/biopython/biopython/issues/3306 here].
* Biopython can use REMARK 465 lines to parse missing residues, see my notebook `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo] ( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]). Also see [https://github.com/biopython/biopython/pull/1237 here] and [https://github.com/biopython/biopython/issues/3306 here].
* article associated with it:
* article associated with it: [https://academic.oup.com/nar/article/36/suppl_2/W255/2506064 SEQATOMS] Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
[SEQATOMS: a web tool for identifying missing regions in PDB in sequence context](https://academic.oup.com/nar/article/36/suppl_2/W255/2506064)
* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16. <ref>PMID: 25559128</ref> <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).  
Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.
He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.
BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16.
PMID: 25559128 <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).  
* Missing strings of residues in protein crystal structures.
* Missing strings of residues in protein crystal structures.
Djinovic-Carugo K, Carugo O.Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.<ref>PMID: 28232893 </ref>
Djinovic-Carugo K, Carugo O.Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.<ref>PMID: 28232893 </ref>
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