1fsd: Difference between revisions

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[[Image:1fsd.png|left|200px]]


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==FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES==
The line below this paragraph, containing "STRUCTURE_1fsd", creates the "Structure Box" on the page.
<StructureSection load='1fsd' size='340' side='right'caption='[[1fsd]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1fsd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. The October 2005 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Designer Proteins''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2005_10 10.2210/rcsb_pdb/mom_2005_10]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FSD FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fsd OCA], [https://pdbe.org/1fsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fsd RCSB], [https://www.ebi.ac.uk/pdbsum/1fsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fsd ProSAT]</span></td></tr>
{{STRUCTURE_1fsd|  PDB=1fsd  |  SCENE=  }}
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.


===FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES===
De novo protein design: fully automated sequence selection.,Dahiyat BI, Mayo SL Science. 1997 Oct 3;278(5335):82-7. PMID:9311930<ref>PMID:9311930</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 9311930 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_9311930}}
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</StructureSection>
==About this Structure==
1FSD is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. The October 2005 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Designer Proteins''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2005_10 10.2210/rcsb_pdb/mom_2005_10]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSD OCA].
 
==Reference==
<ref group="xtra">PMID:9311930</ref><references group="xtra"/>
[[Category: Designer Proteins]]
[[Category: Designer Proteins]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Synthetic construct]]
[[Category: Synthetic construct]]
[[Category: Dahiyat, B I.]]
[[Category: Dahiyat BI]]
[[Category: Mayo, S L.]]
[[Category: Mayo SL]]
[[Category: Computational design]]
[[Category: Novel sequence]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 09:15:02 2010''

Latest revision as of 21:36, 29 November 2023

FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURESFULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES

Structural highlights

1fsd is a 1 chain structure with sequence from Synthetic construct. The October 2005 RCSB PDB Molecule of the Month feature on Designer Proteins by David S. Goodsell is 10.2210/rcsb_pdb/mom_2005_10. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.

De novo protein design: fully automated sequence selection.,Dahiyat BI, Mayo SL Science. 1997 Oct 3;278(5335):82-7. PMID:9311930[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science. 1997 Oct 3;278(5335):82-7. PMID:9311930
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