Re: [ccp4bb] Homology modeling
Dear Amit, I don’t think that PROCHECK is the right tool for assessing the quality of a comparative model. It was revolutionary in its time, but the criteria it looks at can mostly be satisfied by energy minimisation even of an incorrect model, especially if you don’t have to simultaneously satisfy experimental data. For evaluating refined experimental models, I would now be inclined to use Molprobity (available from a website, CCP4 and Phenix) or tools built into graphics programs like ISOLDE and coot. Model quality assessment is actually a thriving subfield in the protein modeling community and it has its own category in the CASP modeling challenges. You want to be looking at the methods that have been judged best by seeing how well they perform in blind predictions. Comparative models differ from experimental models in that they haven’t been constrained by the requirement to fit experimental data, so quality assessment has to look at more subtle features like residue environment. The most recent CASP was CASP13, so a good start would be the main model quality assessment evaluation in the special issue from that event: https://onlinelibrary.wiley.com/doi/10.1002/prot.25767. You’ll find a variety of good tools described there. The one we’ve been playing with, in terms of local assessment of model quality for MR, is ProQ3D, which has an online server: http://proq3.bioinfo.se. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 15 Aug 2020, at 00:39, amit gaur wrote: > > Hi All, >I am trying to generate a model using comparative modeling. Can anybody > suggest the quality of the model based on procheck summary. > > +--<<< P R O C H E C K S U M M A R Y > >>>--+ > | > | > | /var/www/PROCHECK/Jobs/7358861/7358861.pdb 1.5 1253 residues > | > | > | > *| Ramachandran plot: 87.9% core 10.2% allow1.4% gener0.4% disall > | > | > | > *| All Ramachandrans: 67 labelled residues (out of1235) > | > +| Chi1-chi2 plots: 3 labelled residues (out of 771) > | > | Side-chain params:5 better 0 inside 0 worse > | > | > | > *| Residue properties: Max.deviation: 4.9 Bad contacts:0 > | > *| Bond len/angle:9.9Morris et al class: 1 1 2 > | > | > | > | G-factors Dihedrals: -0.13 Covalent: -0.07Overall: -0.10 > | > | > | > *| Planar groups:90.0% within limits 10.0% highlighted 13 off graph > | > | > | > > ++ >+ May be worth investigating further. * Worth investigating further. > > > > Thanks, > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Homology modeling
Hi All, I am trying to generate a model using comparative modeling. Can anybody suggest the quality of the model based on procheck summary. +--<<< P R O C H E C K S U M M A R Y >>>--+ || | /var/www/PROCHECK/Jobs/7358861/7358861.pdb 1.5 1253 residues | || *| Ramachandran plot: 87.9% core 10.2% allow1.4% gener0.4% disall | || *| All Ramachandrans: 67 labelled residues (out of1235) | +| Chi1-chi2 plots: 3 labelled residues (out of 771) | | Side-chain params:5 better 0 inside 0 worse | || *| Residue properties: Max.deviation: 4.9 Bad contacts:0 | *| Bond len/angle:9.9Morris et al class: 1 1 2 | || | G-factors Dihedrals: -0.13 Covalent: -0.07Overall: -0.10 | || *| Planar groups:90.0% within limits 10.0% highlighted 13 off graph | || ++ + May be worth investigating further. * Worth investigating further. Thanks, To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] homology modeling of dimeric proteins
Have you tried with Interactome3D? http://interactome3d.irbbarcelona.org Best, Roberto
Re: [ccp4bb] homology modeling of dimeric proteins
I have successfully used modeller (standalone software; Sali lab) to generate multimeric complexes up to 24-mers Hope tis helps From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudipta Bhattacharyya Sent: Friday, 22 March 2013 5:00 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] homology modeling of dimeric proteins Dear All, Could annyone please suggest me any program or server that can build homology based models of dimeric/oligomeric proteins? Previously I have used many software/servers which can build the monomer of my target proteins but not the dimers. Self docking of homology based monomer is not working in my case since at certain domain one monomer is to some extent wrapped around the adjacent monomer in the template structure. I have also tried the project mode of SWISS-MODEL server but the program is not running with an error message of sequence misalignment; although I think the alignment is fine!!! Please suggest something that would be fruitful. Thanking you in advance for your kind cooperation. Regards, Sudipta Bhattacharyya, Department of Biochemistry and Molecular Biology, Colorado State University.
[ccp4bb] homology modeling of dimeric proteins
Dear All, Could annyone please suggest me any program or server that can build homology based models of dimeric/oligomeric proteins? Previously I have used many software/servers which can build the monomer of my target proteins but not the dimers. Self docking of homology based monomer is not working in my case since at certain domain one monomer is to some extent wrapped around the adjacent monomer in the template structure. I have also tried the project mode of SWISS-MODEL server but the program is not running with an error message of sequence misalignment; although I think the alignment is fine!!! Please suggest something that would be fruitful. Thanking you in advance for your kind cooperation. Regards, Sudipta Bhattacharyya, Department of Biochemistry and Molecular Biology, Colorado State University.
Re: [ccp4bb] homology modeling
Dear Paul! you might want to have a look at http://salilab.org/modeller/ . The stand alone version is free for academia. Christian ___ Dr. Christian Rausch Lehrstuhl für Biologische Chemie Technische Universität München, Germany On Thu, Aug 26, 2010 at 12:03 AM, Paul Kraft wrote: > > Hello, > I've been using an the on-line homology modeling program Jigsaw-3D, and would > like to run it on my own Linux box, but it requires CHARM, which I am > unvailable to get because I am currently looking for a faculty position... > does anyone know of an open source energy minimization program that can be > substituted for CHARM (will GROMOS from SWISS PROT work?). Also is their > any open source homology modeling program that includes solvent interactions > in the minimization (it seems they all require $$, at least the good one's). > Thanks in advance. > Paul > > Dr. Paul Kraft > Structural Biologist > cell 586-596-2770 > email: haresea...@yahoo.com > > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use of the > intended recipient(s). If you are not the intended recipient(s) please note > that any form of disclosure, distribution, copying or use of this > communication or the information in it or in any attachments is strictly > prohibited and may be unlawful. If you have received this communication in > error, please notify the sender and delete the email and destroy any copies > of it. > > E-mail communications cannot be guaranteed to be secure or error free, as > information could be intercepted, corrupted, amended, lost, destroyed, arrive > late or incomplete, or contain viruses. We do not accept liability for any > such matters or their consequences. Anyone who communicates with us by e-mail > is taken to accept the risks in doing so.
[ccp4bb] homology modeling
Hello, I've been using an the on-line homology modeling program Jigsaw-3D, and would like to run it on my own Linux box, but it requires CHARM, which I am unvailable to get because I am currently looking for a faculty position... does anyone know of an open source energy minimization program that can be substituted for CHARM (will GROMOS from SWISS PROT work?). Also is their any open source homology modeling program that includes solvent interactions in the minimization (it seems they all require $$, at least the good one's). Thanks in advance. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Re: [ccp4bb] homology modeling
A metaserver such as bioinfobank is helpful if your sequence is not super-secret, especially if one is not an experienced modeller. http://meta.bioinfo.pl/submit_wizard.pl It submits your sequence to a range of sequence-based and threading- based servers. Models (c-alpha, built with modeller) can be downloaded, inspected, and compared. Alignment files for input to modeller can also be downloaded, allowing you to easily build all-atom models. Sue Dr. Sue A. Roberts Biochemistry & Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [ccp4bb] homology modeling
On 12:08 Tue 05 May , Anastassis Perrakis wrote: > Modeller is indeed an excellent program (so are some others) but, > without being an expert, I was told some time ago and I am still under > the impression, that homology modeling with 20% identity (and many > insertions and deletions as you point out) is a dark art. Being able to > suggest the identical fold with some threading algorithm, is likely all > you will be able to do. A homology based model might be too much to ask. Try HHpred. It will do a profile-profile alignment (well, technically HMM-HMM) and optionally create a multiple-template-based model using Modeller, all with very little knowledge or input required on the user end. Evaluating the likely correctness afterwards is a different story... -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpWMs80Q7nEF.pgp Description: PGP signature
Re: [ccp4bb] homology modeling
Hi, With 20% identity the main problem is the sequence alignment. Usually programs that based only sequence data are not enough in such cases and you need to add additional terms to get the "correct" structure (e.g. threading). You can see list of such programs in our site http://bip.weizmann.ac.il/toolbox/structure/3d.htm Try also to work on the sequence alignment by doing multiple sequence alignment (and not just pair alignment) for selected group of sequences. You can use for that programs like TCoffee packege (http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) , Consensus Server (http://structure.bu.edu/cgi-bin/consensus/ consensus.cgi) and maybe to add structural information to the alignment (e.g. predicted secondary structure) like in Promals3D (http://prodata.swmed.edu/promals3d/promals3d.php) after you have good alignment, the building is straight forward in any homology building program. Gap and insertion are usually in protein loops and they will be always the weak part of your building Good Luck Rotem On 5 May, 2009, at 12:08, Anastassis Perrakis wrote: Suppose I have two proteins A and B, they are structurally homologous, however the sequence identity is only about 20%. A has crystal structure available, so if I want to model protein B, what's the best way to do it? I don't think I can just thread the sequence of B to A structure because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs? -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K. P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 --- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel.
Re: [ccp4bb] homology modeling
Try Phyre (http://www.sbg.bio.ic.ac.uk/phyre/), it worked rather well for some of my projects with very low sequence similarity. Peter On Tue, 5 May 2009 12:08:04 +0300, Anastassis Perrakis wrote: > Modeller is indeed an excellent program (so are some others) but, > without being an expert, I was told some time ago and I am still under > the impression, that homology modeling with 20% identity (and many > insertions and deletions as you point out) is a dark art. Being able > to suggest the identical fold with some threading algorithm, is likely > all you will be able to do. A homology based model might be too much > to ask. > > A. > > On May 5, 2009, at 11:39, Chen, Yu Wai wrote: > >> I would recommend Modeller >> http://www.salilab.org/modeller/ >> >> Wai >>> Suppose I have two proteins A and B, they are structurally >>> homologous, >>> however the sequence identity is only about 20%. A has crystal >>> structure available, so if I want to model protein B, what's the best >>> way to do it? I don't think I can just thread the sequence of B to A >>> structure because the number of residues are different and there >>> might >>> be gaps and insertions in the alignment. Any suggestions of good >>> programs? >>> >> >> >> -- >> Yu Wai Chen, PhDLecturer >> King's College London, Randall Division +44-207-848-8206 >> New Hunt's House, Guy's Campus, London SE1 1UL, U.K. > > P please don't print this e-mail unless you really need to > Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > Department of Biochemistry (B8) > Netherlands Cancer Institute, > Dept. B8, 1066 CX Amsterdam, The Netherlands > Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- Peter Schmidtke -- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona
Re: [ccp4bb] homology modeling
Modeller is indeed an excellent program (so are some others) but, without being an expert, I was told some time ago and I am still under the impression, that homology modeling with 20% identity (and many insertions and deletions as you point out) is a dark art. Being able to suggest the identical fold with some threading algorithm, is likely all you will be able to do. A homology based model might be too much to ask. A. On May 5, 2009, at 11:39, Chen, Yu Wai wrote: I would recommend Modeller http://www.salilab.org/modeller/ Wai Suppose I have two proteins A and B, they are structurally homologous, however the sequence identity is only about 20%. A has crystal structure available, so if I want to model protein B, what's the best way to do it? I don't think I can just thread the sequence of B to A structure because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs? -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K. P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] homology modeling
Hi Rui Very easy to use is EsyPred3D : http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ Also good performance server is 3d-JIGSAW : http://bmm.cancerresearchuk.org/~3djigsaw/ Hope it helps Cheers Francisco > Hi, All > Suppose I have two proteins A and B, they are structurally homologous, > however the sequence identity is only about 20%. A has crystal structure > available, so if I want to model protein B, what's the best way to do it? > I > don't think I can just thread the sequence of B to A structure because the > number of residues are different and there might be gaps and insertions in > the alignment. Any suggestions of good programs? > > Thanks. > > Rui > -- - Francisco J. Enguita, Ph.D. Host-pathogen Interactions Group Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : fengu...@itqb.unl.pt -
Re: [ccp4bb] homology modeling
I would recommend Modeller http://www.salilab.org/modeller/ Wai Suppose I have two proteins A and B, they are structurally homologous, however the sequence identity is only about 20%. A has crystal structure available, so if I want to model protein B, what's the best way to do it? I don't think I can just thread the sequence of B to A structure because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs? -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
[ccp4bb] homology modeling
Hi, All Suppose I have two proteins A and B, they are structurally homologous, however the sequence identity is only about 20%. A has crystal structure available, so if I want to model protein B, what's the best way to do it? I don't think I can just thread the sequence of B to A structure because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs? Thanks. Rui
Re: [ccp4bb] homology modeling----good bond lengths, bad angles
Dear Anagha, just a guess... I'm not sure I understood you properly, but you are only trying to make a model of a solved protein which will lack 3-4 amino acids in a loop... therefore, why not using a modeling soft, such as Coot, remove the amino acids, and do one run of "Regularize Zone"?? You might need to renumber your chain once you have removed the amino acids, but it might work... just a guess... Best regards. Leo On Mar 1, 2007, at 4:11 AM, anagha gupta wrote: Hi CCP4 community! I have constructed a homology model of a deletion variant of a protein whose structure has already been solved. These deletions are 3-4 amino acid in length and are in a loop that connects two helices. The model structures look good with respect to bond lengths in the aforementioned loop region but the bond angles (especially Phi and Psi) are very distorted. Ramachandran plot suggests the same and some of the amino acids flanking the loop are now in the disallowed region. I thought one way to avoid this is to delete one amino acid at a time and construct the model and use the previous model as the template to construct the next model. This is not working very well in fixing the wrong angles. I was wondering if 1) Anybody out there knows good homology modeling software. I used SWISS model and CPH model to create my models. I have heard about prime but right now am waiting to get the software . 2) Is there a way I can fix the angles if I perform an energy minimization of the model. Suggestions are appreciated. Thanks, Anagha. == Chavas Leonard M.G., Ph.D. Structural Research Center KEK,PF. 1-1 Oho Tuskuba, Ibaraki - Japan - PHS: +81(0)29-864-5200 (ext: 2682) e-mail: [EMAIL PROTECTED] URL: http://pfweis.kek.jp/~leo ==
Re: [ccp4bb] homology modeling----good bond lengths, bad angles
Have you tried Modeller ? -Sid. On 2/28/07, anagha gupta <[EMAIL PROTECTED]> wrote: Hi CCP4 community! I have constructed a homology model of a deletion variant of a protein whose structure has already been solved. These deletions are 3-4 amino acid in length and are in a loop that connects two helices. The model structures look good with respect to bond lengths in the aforementioned loop region but the bond angles (especially Phi and Psi) are very distorted. Ramachandran plot suggests the same and some of the amino acids flanking the loop are now in the disallowed region. I thought one way to avoid this is to delete one amino acid at a time and construct the model and use the previous model as the template to construct the next model. This is not working very well in fixing the wrong angles. I was wondering if 1) Anybody out there knows good homology modeling software. I used SWISS model and CPH model to create my models. I have heard about prime but right now am waiting to get the software . 2) Is there a way I can fix the angles if I perform an energy minimization of the model. Suggestions are appreciated. Thanks, Anagha.
[ccp4bb] homology modeling----good bond lengths, bad angles
Hi CCP4 community! I have constructed a homology model of a deletion variant of a protein whose structure has already been solved. These deletions are 3-4 amino acid in length and are in a loop that connects two helices. The model structures look good with respect to bond lengths in the aforementioned loop region but the bond angles (especially Phi and Psi) are very distorted. Ramachandran plot suggests the same and some of the amino acids flanking the loop are now in the disallowed region. I thought one way to avoid this is to delete one amino acid at a time and construct the model and use the previous model as the template to construct the next model. This is not working very well in fixing the wrong angles. I was wondering if 1) Anybody out there knows good homology modeling software. I used SWISS model and CPH model to create my models. I have heard about prime but right now am waiting to get the software . 2) Is there a way I can fix the angles if I perform an energy minimization of the model. Suggestions are appreciated. Thanks, Anagha.
