Re: [ccp4bb] New Version of the Protein Geometry Database Now Available
I think the ref below may be exactly what I am looking for--thanks everyone for your help. Even when the tips were not exactly what I needed, I learned about many tools out there which I may use some day. Generally, I am always impressed by the collegiality and readiness-to-help of all of those who routinely respond to the queries herein. Three cheers for CCP4BB! Jacob Keller Nucleic Acids Res. 2009 Jul;37(Web Server issue):W459-64. doi: 10.1093/nar/gkp304. Epub 2009 May 5. RASMOT-3D PRO: a 3D motif search webserver. Debret G1, Martel A, Cuniasse P. Abstract Detection of structural motif of residues in protein structures allows identification of structural or functional similarity between proteins. In the field of protein engineering, structural motif identification is essential to select protein scaffolds on which a motif of residues can be transferred to design a new protein with a given function. We describe here the RASMOT-3D PRO webserver (http://biodev.extra.cea.fr/rasmot3d/) that performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on Calpha and Cbeta atoms in two steps: inter-atomic distances and RMSD. RASMOT-3D PRO takes in input a PDB file containing the 3D coordinates of the searched motif and provides an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched. Each solution can be graphically examined on the website. The topological search can be conducted in structures described in PDB files uploaded by the user or in those deposited in the PDB. This characteristic as well as the possibility to reject scaffolds sterically incompatible with the target, makes RASMOT-3D PRO a unique webtool in the field of protein engineering. PMID: 19417073 [PubMed - indexed for MEDLINE] PMCID: PMC2703991
Re: [ccp4bb] New Version of the Protein Geometry Database Now Available
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The Protein Geometry Database looks at proteins as collections of bond lengths, angles, and torsion angles. It is not the place to go when you want to know how a protein part is related in space to some other (covalently) distant part. Andy tells me that Jacque Fetrow, who was at Wake Forest University, has a database that might answer your query. There is a paper at J Mol Biol. 2003 Nov 28;334(3):387-401. Structure-based active site profiles for genome analysis and functional family subclassification. Neither one of us has used it. Hope that helps, Dale Tronrud On 6/27/2014 1:49 PM, Keller, Jacob wrote: I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some other software which could be used for this? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Friday, June 27, 2014 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New Version of the Protein Geometry Database Now Available Protein Geometry Database Server V 1.0 http://pgd.science.oregonstate.edu/ Developed by Andy Karplus' laboratory at Oregon State University We are pleased to announce the availability of an enhanced version of the Protein Geometry Database (PGD) web service, originally announced in Berkholz et al (2010) Nucleic Acids Research 38, D320-5. This server allows you to explore the many backbone and side chain conformations that exist in the PDB as well as the protein geometry (lengths and angles) that occur in those conformations. This service is ideal for finding instances of particular conformations or peculiar bond lengths or angles. It is also quite adept at identifying sets of fragments that can then be examined for systematic variation in ideal geometry. The expanded PGD now includes all conformational and covalent geometry information not just for the backbone but also for the sidechains. There are three basic operations available: selecting a set of fragments via a delimited search, analyzing the geometry of those fragments, and dumping the results to your computer for more specialized analysis. To control bias in statistical analyses due to the variable number of entries with the same or similar sequence, the database contains only the highest quality model in each sequence cluster as identified by the Pisces server from Roland Dunbrack's lab. Two settings, 90% and 25% sequence identity, are available. Currently, at the 90% sequence identity level there are 16,000 chains and at the 25% level this drops to about 11,000 chains. You can filter a search based on the quality of the model as indicated by resolution and R values. A search can also be filtered based on DSSP secondary structure, amino acid type, the phi/psi/omega angles and bond lengths, angles, and chi angles. For example, you can find all cysteine residues in the center of three-residue peptide fragments (i.e. not at a peptide terminus), in beta sheet, with both peptide bonds trans, and CB-SG length greater than 1.85 A from models with resolution better than 1.5 A. By the way, in the no more than 25% sequence identity category there are 25 of them. Once you have a set of results, you can create 2D plots showing the relationships of up to three features (i.e. bond lengths, bond angles, or conformational angles). For instance, you can look at how a given feature varies with phi and psi using a phi(i)/psi(i) plot. Or, you can just as easily look at the variation with psi(i)/phi(i+1), or even the relationships between any selected bond angles. As one example, it is instructive to perform a default search and plot NCaCb vs NCaC colored based on CbCaC. As this search is restricted to just the highest resolution models, you can see the justification for chiral volume restraints. Finally, all of your results can be downloaded for your own analysis. Development of the PGD continues. If you have worked with the site and have any ideas and suggestions for how to improvement it, please drop us a line. The publication describing the PGD is: Berkholz, D.S., Krenesky, P.B., Davidson, J.R., Karplus, P.A. (2010) Protein Geometry Database: A flexible engine to explore backbone conformations and their relationships with covalent geometry. Nucleic Acids Res. 38, D320-5. Also, some examples of published analyses enabled by earlier versions of the PGD are listed here:. Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L.J. Karplus, P.A. (2009). Conformation dependence of backbone geometry in proteins. Structure 17, 1316-1325. Hollingsworth, S.A., Berkholz, D.S. Karplus, P.A. (2009). On the occurrence
Re: [ccp4bb] New Version of the Protein Geometry Database Now Available
Jacob Keller There is a service that will hopefully do the calculation you want, search for a template of residues (eg. catalytic-triads). This is just a through space superposition of atoms. It is part of a tool set of fragments found by knowledge based analysis (pdbetemplate) http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ and there is a tool called DB search accessible from this page , or directly from here... http://www.ebi.ac.uk/pdbe-as/pdbesearch/PDBeSearch.jsp You can upload a small template of residues (up to 6) in PDB format using the [upload and analyse] button. The search is weighted based on occupancy - where weights for each atom a defined by the occupancy value. You can specify to just the CA atoms, the side chain (based on occupancy), and use fuzzy matching (slow) where ASP looks like GLU etc. Here is an example PDB file fragment you can use to try out the search - it is a catalytic quartet of residues - a superset of the catalytic triad. Regards Tom Oldfield, PDBe. HEADERHYDROLASE (SERINE PROTEINASE) 22-JAN-85 5CHA 5CHA 3 COMPNDALPHA CHYMOTRYPSIN A (E.C.3.4.21.1) 5CHA 4 SOURCECOW (BOS $TAURUS) 5CHA 5 AUTHOR R.A.BLEVINS,A.TULINSKY 5CHA 6 SITE 1 CTA 3 HIS A 57 ASP A 102 SER A 195 5CHA 160 ATOM403 N HIS A 57 28.981 28.453 20.681 1.00 10.49 5CHA 550 ATOM404 CA HIS A 57 28.691 28.510 22.151 1.00 10.51 5CHA 551 ATOM405 C HIS A 57 29.897 28.096 22.990 1.00 11.71 5CHA 552 ATOM406 O HIS A 57 29.926 28.441 24.252 1.00 11.27 5CHA 553 ATOM407 CB HIS A 57 27.441 27.724 22.518 1.00 10.23 5CHA 554 ATOM408 CG HIS A 57 27.711 26.268 22.692 1.00 11.48 5CHA 555 ATOM409 ND1 HIS A 57 27.449 25.299 21.720 1.00 11.56 5CHA 556 ATOM410 CD2 HIS A 57 28.206 25.605 23.753 1.00 10.62 5CHA 557 ATOM411 CE1 HIS A 57 27.787 24.143 22.229 1.00 12.29 5CHA 558 ATOM412 NE2 HIS A 57 28.219 24.290 23.459 1.00 12.00 5CHA 559 ATOM729 N ASN A 100 21.139 29.092 17.682 1.00 15.17 5CHA 876 ATOM730 CA ASN A 100 21.091 28.846 16.199 1.00 14.91 5CHA 877 ATOM731 C ASN A 100 22.361 29.384 15.589 1.00 14.15 5CHA 878 ATOM732 O ASN A 100 22.993 30.366 16.007 1.00 14.62 5CHA 879 ATOM733 CB ASN A 100 19.865 29.473 15.542 1.00 14.99 5CHA 880 ATOM734 CG ASN A 100 19.459 28.894 14.195 1.00 15.90 5CHA 881 ATOM735 OD1 ASN A 100 19.768 27.721 13.910 1.00 15.64 5CHA 882 ATOM736 ND2 ASN A 100 18.776 29.679 13.303 1.00 15.91 5CHA 883 ATOM745 N ASP A 102 25.217 27.828 15.245 1.00 8.90 5CHA 892 ATOM746 CA ASP A 102 26.263 27.454 16.230 1.00 8.03 5CHA 893 ATOM747 C ASP A 102 27.602 26.986 15.681 1.00 7.56 5CHA 894 ATOM748 O ASP A 102 28.030 25.875 15.937 1.00 6.97 5CHA 895 ATOM749 CB ASP A 102 25.612 26.547 17.282 1.00 7.61 5CHA 896 ATOM750 CG ASP A 102 26.373 26.259 18.576 1.00 7.61 5CHA 897 ATOM751 OD1 ASP A 102 26.215 25.289 19.348 1.00 6.70 5CHA 898 ATOM752 OD2 ASP A 102 27.250 27.077 18.886 1.00 7.66 5CHA 899 ATOM 1404 N SER A 195 30.503 18.936 23.287 1.00 10.84 5CHA1551 ATOM 1405 CA SER A 195 30.268 20.144 22.534 1.00 11.39 5CHA1552 ATOM 1406 C SER A 195 31.398 20.500 21.546 1.00 11.49 5CHA1553 ATOM 1407 O SER A 195 32.602 20.510 21.836 1.00 10.92 5CHA1554 ATOM 1408 CB SER A 195 30.081 21.398 23.463 1.00 11.44 5CHA1555 ATOM 1409 OG SER A 195 28.708 21.332 23.826 1.00 13.00 5CHA1556 On 27/06/14 21:49, Keller, Jacob wrote: I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some other software which could be used for this? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Friday, June 27, 2014 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New Version of the Protein Geometry Database Now Available -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Protein Geometry Database Server V 1.0 http://pgd.science.oregonstate.edu/ Developed by Andy Karplus' laboratory at Oregon State University We are pleased to announce the availability of an enhanced version of the Protein Geometry Database (PGD) web service, originally
[ccp4bb] New Version of the Protein Geometry Database Now Available
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Protein Geometry Database Server V 1.0 http://pgd.science.oregonstate.edu/ Developed by Andy Karplus' laboratory at Oregon State University We are pleased to announce the availability of an enhanced version of the Protein Geometry Database (PGD) web service, originally announced in Berkholz et al (2010) Nucleic Acids Research 38, D320-5. This server allows you to explore the many backbone and side chain conformations that exist in the PDB as well as the protein geometry (lengths and angles) that occur in those conformations. This service is ideal for finding instances of particular conformations or peculiar bond lengths or angles. It is also quite adept at identifying sets of fragments that can then be examined for systematic variation in ideal geometry. The expanded PGD now includes all conformational and covalent geometry information not just for the backbone but also for the sidechains. There are three basic operations available: selecting a set of fragments via a delimited search, analyzing the geometry of those fragments, and dumping the results to your computer for more specialized analysis. To control bias in statistical analyses due to the variable number of entries with the same or similar sequence, the database contains only the highest quality model in each sequence cluster as identified by the Pisces server from Roland Dunbrack's lab. Two settings, 90% and 25% sequence identity, are available. Currently, at the 90% sequence identity level there are 16,000 chains and at the 25% level this drops to about 11,000 chains. You can filter a search based on the quality of the model as indicated by resolution and R values. A search can also be filtered based on DSSP secondary structure, amino acid type, the phi/psi/omega angles and bond lengths, angles, and chi angles. For example, you can find all cysteine residues in the center of three-residue peptide fragments (i.e. not at a peptide terminus), in beta sheet, with both peptide bonds trans, and CB-SG length greater than 1.85 A from models with resolution better than 1.5 A. By the way, in the no more than 25% sequence identity category there are 25 of them. Once you have a set of results, you can create 2D plots showing the relationships of up to three features (i.e. bond lengths, bond angles, or conformational angles). For instance, you can look at how a given feature varies with phi and psi using a phi(i)/psi(i) plot. Or, you can just as easily look at the variation with psi(i)/phi(i+1), or even the relationships between any selected bond angles. As one example, it is instructive to perform a default search and plot NCaCb vs NCaC colored based on CbCaC. As this search is restricted to just the highest resolution models, you can see the justification for chiral volume restraints. Finally, all of your results can be downloaded for your own analysis. Development of the PGD continues. If you have worked with the site and have any ideas and suggestions for how to improvement it, please drop us a line. The publication describing the PGD is: Berkholz, D.S., Krenesky, P.B., Davidson, J.R., Karplus, P.A. (2010) Protein Geometry Database: A flexible engine to explore backbone conformations and their relationships with covalent geometry. Nucleic Acids Res. 38, D320-5. Also, some examples of published analyses enabled by earlier versions of the PGD are listed here:. Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L.J. Karplus, P.A. (2009). Conformation dependence of backbone geometry in proteins. Structure 17, 1316-1325. Hollingsworth, S.A., Berkholz, D.S. Karplus, P.A. (2009). On the occurrence of linear groups in proteins. Protein Science 18, 1321-1325 Hollingsworth, S.A. Karplus, P. A. (2010). Review: A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. BioMolecular Concepts 1, 271-283. Berkholz, D.S., Driggers, C.M., Shapovalov, M.V., Dunbrack, R.L., Jr. Karplus P.A. (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A. 109, 449-53. Dale Tronrud P. Andrew Karplus Department of Biochemistry and Biophysics Oregon State University -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlOt044ACgkQU5C0gGfAG12aZACdG68Vyjw7JJimw0ofMZrJQLu8 B1IAn0Q5xx8ptRosgMXswdYmdjNKyFkA =D63d -END PGP SIGNATURE-
Re: [ccp4bb] New Version of the Protein Geometry Database Now Available
I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some other software which could be used for this? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Friday, June 27, 2014 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New Version of the Protein Geometry Database Now Available -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Protein Geometry Database Server V 1.0 http://pgd.science.oregonstate.edu/ Developed by Andy Karplus' laboratory at Oregon State University We are pleased to announce the availability of an enhanced version of the Protein Geometry Database (PGD) web service, originally announced in Berkholz et al (2010) Nucleic Acids Research 38, D320-5. This server allows you to explore the many backbone and side chain conformations that exist in the PDB as well as the protein geometry (lengths and angles) that occur in those conformations. This service is ideal for finding instances of particular conformations or peculiar bond lengths or angles. It is also quite adept at identifying sets of fragments that can then be examined for systematic variation in ideal geometry. The expanded PGD now includes all conformational and covalent geometry information not just for the backbone but also for the sidechains. There are three basic operations available: selecting a set of fragments via a delimited search, analyzing the geometry of those fragments, and dumping the results to your computer for more specialized analysis. To control bias in statistical analyses due to the variable number of entries with the same or similar sequence, the database contains only the highest quality model in each sequence cluster as identified by the Pisces server from Roland Dunbrack's lab. Two settings, 90% and 25% sequence identity, are available. Currently, at the 90% sequence identity level there are 16,000 chains and at the 25% level this drops to about 11,000 chains. You can filter a search based on the quality of the model as indicated by resolution and R values. A search can also be filtered based on DSSP secondary structure, amino acid type, the phi/psi/omega angles and bond lengths, angles, and chi angles. For example, you can find all cysteine residues in the center of three-residue peptide fragments (i.e. not at a peptide terminus), in beta sheet, with both peptide bonds trans, and CB-SG length greater than 1.85 A from models with resolution better than 1.5 A. By the way, in the no more than 25% sequence identity category there are 25 of them. Once you have a set of results, you can create 2D plots showing the relationships of up to three features (i.e. bond lengths, bond angles, or conformational angles). For instance, you can look at how a given feature varies with phi and psi using a phi(i)/psi(i) plot. Or, you can just as easily look at the variation with psi(i)/phi(i+1), or even the relationships between any selected bond angles. As one example, it is instructive to perform a default search and plot NCaCb vs NCaC colored based on CbCaC. As this search is restricted to just the highest resolution models, you can see the justification for chiral volume restraints. Finally, all of your results can be downloaded for your own analysis. Development of the PGD continues. If you have worked with the site and have any ideas and suggestions for how to improvement it, please drop us a line. The publication describing the PGD is: Berkholz, D.S., Krenesky, P.B., Davidson, J.R., Karplus, P.A. (2010) Protein Geometry Database: A flexible engine to explore backbone conformations and their relationships with covalent geometry. Nucleic Acids Res. 38, D320-5. Also, some examples of published analyses enabled by earlier versions of the PGD are listed here:. Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L.J. Karplus, P.A. (2009). Conformation dependence of backbone geometry in proteins. Structure 17, 1316-1325. Hollingsworth, S.A., Berkholz, D.S. Karplus, P.A. (2009). On the occurrence of linear groups in proteins. Protein Science 18, 1321-1325 Hollingsworth, S.A. Karplus, P. A. (2010). Review: A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. BioMolecular Concepts 1, 271-283. Berkholz, D.S., Driggers, C.M., Shapovalov, M.V., Dunbrack, R.L., Jr. Karplus P.A. (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A. 109, 449-53. Dale Tronrud P. Andrew Karplus Department of Biochemistry and Biophysics Oregon State University -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32
