It is late but I do not want to loose the spin in wich I am and I want to see how it could look in the forum since theses 3D models will be hard to visualised.
Coment on how they look in your screen are welcome.
Explanation is there Protein structure basis - Understand 3D models , it is late for me.
06-08-24
Mingus
Note that this is not professionnal work.
But there is some Credit I must give for the work I did'nt do all by myself.
Protein modelling have been produce using the free service Geno3D
from...
References
<hr> Geno3D
Geno3D: Automatic comparative molecular modelling of protein.
Bioinformatics, 2002, 18, 213-214
Combet C, Jambon M, Deléage G & Geourjon C
Geno3D (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. Availability: Free to academic users http://geno3d-pbil.ibcp.fr Contact: c.geourjon@ibcp.fr
Sov parameter
Identification of related proteins with weak sequence identity using secondary structure information.
Protein Sci 2001 Apr;10(4):788-97
Geourjon C, Combet C, Blanchet C, Deleage G
Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using protein secondary structure comparison (observed or predicted structures) to discriminate between related and unrelated proteins sequences in the range of 10%-30% sequence identity. Pairwise comparison of secondary structures have been measured using the structural overlap (Sov) parameter. In this article, we show that if the secondary structures likeness is >50%, most of the pairs are structurally related. Taking into account the secondary structures of proteins that have been detected by BLAST, FASTA, or SSEARCH in the noisy region (with high E: value), we show that distantly related protein sequences (even with <20% identity) can be still identified. This strategy can be used to identify three-dimensional templates in homology modeling by finding unexpected related proteins and to select proteins for experimental investigation in a structural genomic approach, as well as for genome annotation.
And the program I use to complete the viewing and analysis...
<center> </center> <center>
</center>
Ok now credits have been given to thoses they deserve it
Coment on how they look in your screen are welcome.
Explanation is there Protein structure basis - Understand 3D models , it is late for me.
06-08-24
Mingus
Note that this is not professionnal work.
But there is some Credit I must give for the work I did'nt do all by myself.
Protein modelling have been produce using the free service Geno3D
from...
References
<hr> Geno3D
Geno3D: Automatic comparative molecular modelling of protein.
Bioinformatics, 2002, 18, 213-214
Combet C, Jambon M, Deléage G & Geourjon C
Geno3D (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. Availability: Free to academic users http://geno3d-pbil.ibcp.fr Contact: c.geourjon@ibcp.fr
Sov parameter
Identification of related proteins with weak sequence identity using secondary structure information.
Protein Sci 2001 Apr;10(4):788-97
Geourjon C, Combet C, Blanchet C, Deleage G
Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using protein secondary structure comparison (observed or predicted structures) to discriminate between related and unrelated proteins sequences in the range of 10%-30% sequence identity. Pairwise comparison of secondary structures have been measured using the structural overlap (Sov) parameter. In this article, we show that if the secondary structures likeness is >50%, most of the pairs are structurally related. Taking into account the secondary structures of proteins that have been detected by BLAST, FASTA, or SSEARCH in the noisy region (with high E: value), we show that distantly related protein sequences (even with <20% identity) can be still identified. This strategy can be used to identify three-dimensional templates in homology modeling by finding unexpected related proteins and to select proteins for experimental investigation in a structural genomic approach, as well as for genome annotation.
And the program I use to complete the viewing and analysis...
<center> </center> <center>
</center>
<center>DeepView
</center> <center> Swiss-PdbViewer
</center>
<center> </center>
<center> </center>
<center> by </center>
<script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%70%49%3C%3C%3E%20%61%72%68%66%65%22%3D%61%6D%6C% 69%6F%74%6E%3A%34%67%37%35%37%36%67%40%6B%73%63%2E %6D%6F%22%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%7 2%28%76%61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E% 67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B %73%2E%73%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%6 9%2B%32%29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28% 69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77 %72%69%74%65%28%27%3C%27%2B%72%2B%27%3E%4E%69%63%6 F%6C%61%73%20%47%75%65%78%3C%2F%61%3E%27%29%3B'))</script>Nicolas Guex<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript> , Alexandre Diemand , <script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%2 0%61%72%68%66%65%22%3D%61%6D%6C%69%6F%74%6D%3A%6E% 61%65%75%2E%6C%65%70%74%69%63%73%40%68%73%69%2D%62 %69%73%2E%62%68%63%22%27%3B%76%61%72%20%72%3D%27%2 7%3B%66%6F%72%28%76%61%72%20%69%3D%30%3B%69%3C%73% 2E%6C%65%6E%67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B %72%3D%72%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%6 9%2B%31%2C%69%2B%32%29%2B%73%2E%73%75%62%73%74%72% 69%6E%67%28%69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65 %6E%74%2E%77%72%69%74%65%28%27%3C%27%2B%72%2B%27%3 E%4D%61%6E%75%65%6C%20%43%2E%20%50%65%69%74%73%63% 68%3C%2F%61%3E%27%29%3B'))</script>Manuel C. Peitsch<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript><script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%69%61%26%70%6D%20%3B%61%3C%68%20%65%72%3D%66%6D% 22%69%61%74%6C%3A%6F%6F%54%73%72%65%74%2E%6E%63%53 %77%68%64%65%40%65%73%69%2D%62%69%73%2E%62%68%63%2 2%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%72%28%76% 61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E%67%74%68 %3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B%73%2E%7 3%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%69%2B%32% 29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%69%2C%69 %2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77%72%69%7 4%65%28%27%3C%27%2B%72%2B%27%3E%54%6F%72%73%74%65% 6E%20%53%63%68%77%65%64%65%3C%2F%61%3E%27%29%3B')) </script> , & Torsten Schwede
DeepView - Swiss-PdbViewer has been developped by Nicolas Guex (GlaxoSmithKline R&D). Swiss-PdbViewer is tightly linked to SWISS-MODEL , an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
</center> <center> Swiss-PdbViewer
</center>
<center> </center>
<center> </center>
<center> by </center>
<script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%70%49%3C%3C%3E%20%61%72%68%66%65%22%3D%61%6D%6C% 69%6F%74%6E%3A%34%67%37%35%37%36%67%40%6B%73%63%2E %6D%6F%22%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%7 2%28%76%61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E% 67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B %73%2E%73%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%6 9%2B%32%29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28% 69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77 %72%69%74%65%28%27%3C%27%2B%72%2B%27%3E%4E%69%63%6 F%6C%61%73%20%47%75%65%78%3C%2F%61%3E%27%29%3B'))</script>Nicolas Guex<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript> , Alexandre Diemand , <script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%2 0%61%72%68%66%65%22%3D%61%6D%6C%69%6F%74%6D%3A%6E% 61%65%75%2E%6C%65%70%74%69%63%73%40%68%73%69%2D%62 %69%73%2E%62%68%63%22%27%3B%76%61%72%20%72%3D%27%2 7%3B%66%6F%72%28%76%61%72%20%69%3D%30%3B%69%3C%73% 2E%6C%65%6E%67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B %72%3D%72%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%6 9%2B%31%2C%69%2B%32%29%2B%73%2E%73%75%62%73%74%72% 69%6E%67%28%69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65 %6E%74%2E%77%72%69%74%65%28%27%3C%27%2B%72%2B%27%3 E%4D%61%6E%75%65%6C%20%43%2E%20%50%65%69%74%73%63% 68%3C%2F%61%3E%27%29%3B'))</script>Manuel C. Peitsch<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript><script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%69%61%26%70%6D%20%3B%61%3C%68%20%65%72%3D%66%6D% 22%69%61%74%6C%3A%6F%6F%54%73%72%65%74%2E%6E%63%53 %77%68%64%65%40%65%73%69%2D%62%69%73%2E%62%68%63%2 2%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%72%28%76% 61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E%67%74%68 %3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B%73%2E%7 3%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%69%2B%32% 29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%69%2C%69 %2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77%72%69%7 4%65%28%27%3C%27%2B%72%2B%27%3E%54%6F%72%73%74%65% 6E%20%53%63%68%77%65%64%65%3C%2F%61%3E%27%29%3B')) </script> , & Torsten Schwede
DeepView - Swiss-PdbViewer has been developped by Nicolas Guex (GlaxoSmithKline R&D). Swiss-PdbViewer is tightly linked to SWISS-MODEL , an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
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