User:Wayne Decatur/Structure analysis tools: Difference between revisions
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* 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/ | * 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/ | ||
* 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]). | * 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]). | ||
* 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> | |||
* Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. DeForte S, Uversky VN.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. <ref>PMID: 26683124</ref> | * Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. DeForte S, Uversky VN.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. <ref>PMID: 26683124</ref> | ||
