The following two plots are made according to the statistical values provided by the Richardson group. I download the KINEMAGE format of Glycine and Proline. Inside the two files, core and allowed regions are defined and can be extracted to make my own Ramachandran plot. The defined core and allowed regions are also shown in [...]
[KPWU blog] Examples of Ramachandran plots of residues in helix, strand or coil regions
Examples of Ramachandran plots of residues in helix, strand or coil regions
Few weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played around and try to use GnuPlot 4.4 to make my own Ramachandran plots. Here are three examples of the residual Ramachandran space regarding to the helical, extend or coil regions. I used STRIDE to http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=372&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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05-10-2011 07:07 AM
[KPWU blog] Making Ramachandran plot ?II
Making Ramachandran plot ?II
Long time ago, I made a blog article at here to make a record where I can go back to dig information of Ramachandran plot. But the ranges used in the Ramachandran plot are a bit out of date. The Richardson group has a publication in 2003*(Structure validation by Calpha geometry: phi,psi and Cbeta deviation http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=349&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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04-20-2011 02:51 AM
[NMR paper] Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein C
Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains.
Related Articles Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains.
J Mol Biol. 1999 Oct 1;292(4):893-908
Authors: Kloiber K, Weiskirchen R, Kräutler B, Bister K, Konrat R
The LIM domain is a conserved cysteine and histidine-containing structural module of two tandemly arranged zinc fingers. It has been...
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11-18-2010 08:31 PM
[NMR paper] NMR structural characterization of oligo-N-substituted glycine lead compounds from a
NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library.
Related Articles NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library.
Mol Divers. 1997;3(1):1-15
Authors: Bradley EK, Kerr JM, Richter LS, Figliozzi GM, Goff DA, Zuckermann RN, Spellmeyer DC, Blaney JM
Synthesis and screening of combinatorial libraries for pharmaceutical lead discovery is a rapidly expanding field. Oligo-N-substituted glycines (NSGs) were one of the earliest sources...
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08-22-2010 03:31 PM
[NMR paper] NMR structural characterization of oligo-N-substituted glycine lead compounds from a
NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library.
Related Articles NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library.
Mol Divers. 1997;3(1):1-15
Authors: Bradley EK, Kerr JM, Richter LS, Figliozzi GM, Goff DA, Zuckermann RN, Spellmeyer DC, Blaney JM
Synthesis and screening of combinatorial libraries for pharmaceutical lead discovery is a rapidly expanding field. Oligo-N-substituted glycines (NSGs) were one of the earliest sources...
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08-22-2010 03:03 PM
[NMR paper] Proline pipe helix: structure of the tus proline repeat determined by 1H NMR.
Proline pipe helix: structure of the tus proline repeat determined by 1H NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Proline pipe helix: structure of the tus proline repeat determined by 1H NMR.
Biochemistry. 1996 Jan 23;35(3):698-703
Authors: Butcher DJ, Nedved ML, Neiss TG, Moe GR
The structure of a 22 amino acid peptide, TPPI , that is similar to the proline repeat segment of the replication arrest protein, Tus, has been determined by 1H NMR in 50% trifluroethanol. The...
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08-22-2010 02:27 PM
[Stan NMR blog] Is every finite-dimensional Hilbert space a spin-space?
Is every finite-dimensional Hilbert space a spin-space?
Every linear operator on any finite Hilbert space can be generated from spin operators.
More...
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08-21-2010 06:14 PM
Got bad PROCHECK Ramachandran plot? Try MolProbity
Don't get good numbers of Ramachandran plot for your protein when you use PROCHEK-NMR? This could be because PROCHEK most favored regions of Ramachandran plot are too small, not because your model is bad. Try to check your protein using MolProbity server from Richardson's lab.
Ramachandran space of Glycine and Proline
Linear Mode
