User:Eric Martz/Sandbox 11

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Proposed page title: <big>'''Structural Alignment Tools'''</big>
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<big><b>Proposed title: Knots in Proteins: Methods</b></big>
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<br>
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''Structural alignment'' refers to the alignment, in three dimensions, between two or more molecular models. In the case of proteins, this is usually performed without reference to the sequences of the proteins.
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Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structural alignment software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structural alignment].
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This page describes technical details of the methods used for the morph at [[Knots in proteins]].
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==Structural Alignment Servers==
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The [[PDB file]] that displays the animated morph of the protein knot being "shrunk" is [[Image:1yve i knot morph.pdb]]. This file contains 51 models. Model 1 is a slightly smoothed backbone trace of the knotted segment of chain I in [[1yve]], namely 234 residues, sequence numbers 312-545. Model 51 is a simplified knot, which is the result of shrinking the backbone while keeping the ends fixed in space. These models were kindly provided by William R. Taylor ([http://mathbio.nimr.mrc.ac.uk/ Division of Mathematical Biology, National Institute for Medical Research, the Ridgeway, Mill Hill, London UK]). These models represent the residues with alpha carbon atoms only, and all residues are labeled GLY.
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Alphabetical, by server name:
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===CE===
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For the [http://www.umass.edu/microbio/chime/knots/ website developed in 2000], the coordinates of these models were reduced (using the MS-DOS [http://www.umass.edu/microbio/rasmol/pdbtools.htm PDB Tools] program shrink.exe) so the visualization plug-in MDL Chime would automatically connect the alpha carbon atoms (some being unrealistically distant from each other) with a backbone trace. However, Jmol did not connect consecutive alpha carbon atoms due to the mixture of unrealistically small and large distances between them. Therefore, the following script was employed to generate bonds (''wireframe'') in Jmol between consecutive alpha carbon atoms:
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The ''Combinatorial Extension'' structural alignment server.
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<pre>select all # all 51 models
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*Server: [http://cl.sdsc.edu/ CE Home Page].
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wireframe off
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*Publication (1998)<ref>PMID: 9796821</ref>
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backbone off
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*'''N.B. Database of structure neighbors has not been updated since 2004. Java applet for viewing results is not working in Sept. 2010. Finding structure neighbors from the entire PDB database ("ALL") appears to have been broken since 2001.'''
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spacefill off
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*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
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connect delete # deletes all the automatically generated inter-atomic bonds
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*Structure-based sequence alignment: YES.
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# now connect consecutive alpha carbons. model 1 contains 234 alpha carbons. model 51 contains 14.
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for (i=1; i<=234; i++)
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{
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ii = i + 1;
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connect (atomno=i) (atomno=ii);
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}
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wireframe 0.05 # display the new connections
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color group</pre>
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===DALI===
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The morph for the comparison example that has no knot, [[1tph]] chain "1", is in [[Image:1tph 1 noknot morph.pdb]]. Similar methods were employed, adjusting the maximum residue count in the above script from 234 to 242.
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*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
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===FATCAT===
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*Server: [http://fatcat.burnham.org/ fatcat.burnham.org] Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
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*Publication (2003)<ref name="fatcat">PMID: 14534198</ref> "... the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges."
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*Help on server: YES with snapshots; some context-sensitive help.
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*Does alignment involve sequence comparison? UNCLEAR.
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*Rigid alignment: YES (optional)
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*Flexible alignment: YES (optional)
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*Structure neighbors (pre-calculated): YES
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*Pairwise alignment including uploaded models: YES
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*Visualization: Jmol or Chime. See ''Special features''.
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*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
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*Offered by RCSB? YES
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*Special features: Produces a morph between the two aligned chains (at the link "Interpolating between ..."). Produces a sequence alignment. Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).
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Notes from the publication: With 10 "difficult examples"<ref>Fischer,D., Elofsson,A., Rice,D. and Eisenberg,D. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In Pacific Symposium on Biocomputing. pp. 300–318.</ref> FATCAT produced results comparable (length, RMSD) to the rigid alignment servers DALI, VAST, CE with no twists in 8 cases. This shows that FATCAT is not biased to introduce twists (hinges). Hinges were introduced in two of the difficult cases, producing arguably better alignments. In a comparison with ''FlexProt''<ref>PMID: 12112693</ref>, FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).
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===FlexProt===
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*Server: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt].
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*Publication (2002)<ref>PMID: 12112693</ref>
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*Rigid alignment: YES (Results include alignment for 0 hinges, but only a well-aligning subset of residues are aligned.)
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*Flexible alignment: YES (Results are given for various numbers of hinges.)
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*Visualization: '''NONE''' (You can download PDB files.)
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*Ligands: '''Discarded'''.
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*Special features: Assigns a distinct chain name to each rigid segment separated by a hinge, facilitating informative coloring.
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Note: [[#FATCAT|FATCAT]] provides evidence that it out-performs FlexProt.
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===MAMMOTH===
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*Server: [http://ub.cbm.uam.es/servers/mammoth/mammoth.php mammoth MAMMOTH] (MAtching Molecular Models Obtained from THeory)
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*Publication (2002)<ref name="mammoth">PMID: 12381844</ref>
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*Help on server: Little or none.
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*Does alignment involve sequence comparison? NO: They state that this is a "sequence-independent structural alignment".
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*Rigid alignment: YES.
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*Flexible alignment: NO.
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*Multiple alignment: YES.
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*Structure neighbors (pre-calculated): NO.
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*Pairwise alignment including uploaded models: YES
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*Visualization: None (you can download a PDB file and a RasMol script. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. There is a PDB file with chains A and B in the downloadable file ''rasmol.tcl'' but this is not a Jmol-ready file.''')
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*Color by deviation: '''NO'''.
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*Offered by RCSB? YES
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===TM-Align===
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*Server: [http://zhanglab.ccmb.med.umich.edu/TM-align/ TM-align]
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*Publication (2005)<ref name="mammoth">PMID: 15849316</ref>
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*Help on server: A little.
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*Does alignment involve sequence comparison? UNCLEAR.
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*Rigid alignment: YES.
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*Flexible alignment: NO.
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*Multiple alignment: You can download the software to run on linux.
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*Structure neighbors (pre-calculated): NO.
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*Pairwise alignment including uploaded models: YES
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*Visualization: None (you can download a script for RasMol that contains PDB coordinates. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. File does not run as a script in Jmol due to REMARK lines that are not legal Jmol commands.''')
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*Color by deviation: '''NO'''.
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*Offered by RCSB? YES
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===TopMatch===
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*Server: [http://topmatch.services.came.sbg.ac.at/ TopMatch]
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*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>
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*Help on server: YES.
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*Does alignment involve sequence comparison? UNCLEAR.
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*Rigid alignment: YES.
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*Flexible alignment: NO.
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*Multiple alignment: NO.
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*Structure neighbors (pre-calculated): NO.
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*Pairwise alignment including uploaded models: YES
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*Visualization: Jmol.
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*Color by deviation: '''NO'''.
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*Offered by RCSB? YES
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*Special features: You can download the aligned target PDB file (in a separate file from the query PDB file). A PyMOL script is also available.
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===VAST===
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Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
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==Structural Alignment Software==
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===Calculate Structure Alignment===
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This is a java program (java web start) offered by the U.S. [[PDB]]. At [http://www.pdb.org the PDB website], look for the box of '''Tools''' on the left hand side, and click on ''Compare Structures''. You will then get a form where you can enter two [[PDB codes]] (or upload two PDB files), optionally with a sequence range for each. Alternatively, with the ''Database Search'' option, you can enter a single PDB code (or upload a PDB file), and find structure neighbors. On the right is a link "Align custom files (Launches a Java Web Start application)", which starts the ''Calculate Structure Alignment'' java software. This package offers java implementations of the CE and FATCAT (you can choose '''rigid''' or '''flexible''') algorithms (see above).
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* Database Search: I got no results after clicking "Align" for either jCE or jFATCAT - rigid. These options did not appear to be working. [[User:Eric Martz|Eric Martz]] 16:28, 4 October 2010 (IST)
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==Examples==
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===Example Requiring Flexibility===
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'''This example requires flexibility for a good alignment''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.
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*CE:
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**4.8 &Aring; RMSD.
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**38.5% sequence identity in structure-based sequence alignment. Aligned/gap positions = 109/47.
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**Uses old, unremediated PDB files (1cfc has no chain A).
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*FATCAT:
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**5 hinges(twists): 140 residues aligned, RMSD 2.08 &Aring;.
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*FlexProt:
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**0 hinges: 49 residues aligned, RMSD 2.94 &Aring;.
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**1 hinge: 84 residues aligned, RMSD 2.97 &Aring;.
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**2 hinges: 102 residues aligned, RMSD 2.82 &Aring;.
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**3 hinges: 118 residues aligned, RMSD 2.60 &Aring;.
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**4 hinges: 134 residues aligned, RMSD 2.62 &Aring;.
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===Example for Rigid Alignment===
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[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin found in [[1tub]] chain A, length 440.
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====CE====
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*3.2 &Aring; RMSD for 305 residues. The structural alignment has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less.
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*12.5% sequence identity.
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====FATCAT====
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*3.02 &Aring; RMSD RIGID alignment includes 298 residues.
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*FLEXIBLE alignment introduced ZERO twists (hinges), so gave the same result as the rigid alignment.
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*The structure-based sequence alignment has many gaps, looking similar to that generated by CE.
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====MAMMOTH====
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*4.0 &Aring; (?) with 298 aligned residues (?) (Labeling in results is unclear.)
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*Structure-based sequence alignment is displayed.
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====TM-Align====
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*3.42 &Aring; for 312 aligned residues.
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*Structure-based sequence alignment is displayed.
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====TopMatch====
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*Error # 1063, no explanation. No structures displayed in Jmol.
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*3.1 &Aring; RMSD. Alignment includes 251 residues. Sequence identity in the aligned regions is 12%.
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*Structure-based sequence alignment is displayed.
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*Tried the example requiring flexibility (above) as a second case. A 40 residue subdomain was aligned with RMSD 1.8 &Aring;, and the alignment was displayed in Jmol with no error.
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==References==
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<references />
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Current revision

Proposed title: Knots in Proteins: Methods

This page describes technical details of the methods used for the morph at Knots in proteins.

The PDB file that displays the animated morph of the protein knot being "shrunk" is Image:1yve i knot morph.pdb. This file contains 51 models. Model 1 is a slightly smoothed backbone trace of the knotted segment of chain I in 1yve, namely 234 residues, sequence numbers 312-545. Model 51 is a simplified knot, which is the result of shrinking the backbone while keeping the ends fixed in space. These models were kindly provided by William R. Taylor (Division of Mathematical Biology, National Institute for Medical Research, the Ridgeway, Mill Hill, London UK). These models represent the residues with alpha carbon atoms only, and all residues are labeled GLY.

For the website developed in 2000, the coordinates of these models were reduced (using the MS-DOS PDB Tools program shrink.exe) so the visualization plug-in MDL Chime would automatically connect the alpha carbon atoms (some being unrealistically distant from each other) with a backbone trace. However, Jmol did not connect consecutive alpha carbon atoms due to the mixture of unrealistically small and large distances between them. Therefore, the following script was employed to generate bonds (wireframe) in Jmol between consecutive alpha carbon atoms: 

select all # all 51 models
wireframe off
backbone off
spacefill off
connect delete # deletes all the automatically generated inter-atomic bonds
# now connect consecutive alpha carbons. model 1 contains 234 alpha carbons. model 51 contains 14.
for (i=1; i<=234; i++)
{
	ii = i + 1;
	connect (atomno=i) (atomno=ii);
}
wireframe 0.05 # display the new connections
color group

The morph for the comparison example that has no knot, 1tph chain "1", is in Image:1tph 1 noknot morph.pdb. Similar methods were employed, adjusting the maximum residue count in the above script from 234 to 242.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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