3auv: Difference between revisions

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<StructureSection load='3auv' size='340' side='right'caption='[[3auv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='3auv' size='340' side='right'caption='[[3auv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3auv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AUV FirstGlance]. <br>
<table><tr><td colspan='2'>[[3auv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AUV FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3auv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3auv OCA], [https://pdbe.org/3auv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3auv RCSB], [https://www.ebi.ac.uk/pdbsum/3auv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3auv ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3auv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3auv OCA], [https://pdbe.org/3auv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3auv RCSB], [https://www.ebi.ac.uk/pdbsum/3auv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3auv ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes.
Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.,Yu CM, Peng HP, Chen IC, Lee YC, Chen JB, Tsai KC, Chen CT, Chang JY, Yang EW, Hsu PC, Jian JW, Hsu HJ, Chang HJ, Hsu WL, Huang KF, Ma AC, Yang AS PLoS One. 2012;7(3):e33340. Epub 2012 Mar 22. PMID:22457753<ref>PMID:22457753</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3auv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Antibody 3D structures|Antibody 3D structures]]
*[[Antibody 3D structures|Antibody 3D structures]]
*[[3D structures of human antibody|3D structures of human antibody]]
*[[3D structures of human antibody|3D structures of human antibody]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chang, H J]]
[[Category: Chang HJ]]
[[Category: Chang, J Y]]
[[Category: Chang JY]]
[[Category: Chen, C T]]
[[Category: Chen CT]]
[[Category: Chen, I C]]
[[Category: Chen IC]]
[[Category: Chen, J B]]
[[Category: Chen JB]]
[[Category: Hsu, H J]]
[[Category: Hsu HJ]]
[[Category: Hsu, P C]]
[[Category: Hsu PC]]
[[Category: Hsu, W L]]
[[Category: Hsu WL]]
[[Category: Huang, K F]]
[[Category: Huang KF]]
[[Category: Jian, J W]]
[[Category: Jian JW]]
[[Category: Lee, Y C]]
[[Category: Lee YC]]
[[Category: Ma, A C]]
[[Category: Ma AC]]
[[Category: Peng, H P]]
[[Category: Peng HP]]
[[Category: Tsai, K C]]
[[Category: Tsai KC]]
[[Category: Yang, A S]]
[[Category: Yang AS]]
[[Category: Yang, E W]]
[[Category: Yang EW]]
[[Category: Yu, C M]]
[[Category: Yu CM]]
[[Category: Antibody engineering]]
[[Category: Immune system]]
[[Category: Monovalent antibody]]
[[Category: Scfv]]
[[Category: Vegf]]

Latest revision as of 11:40, 7 February 2024

Predicting Amino Acid Preferences in the Complementarity Determining Regions of an Antibody-Antigen Recognition InterfacePredicting Amino Acid Preferences in the Complementarity Determining Regions of an Antibody-Antigen Recognition Interface

Structural highlights

3auv is a 6 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3auv, resolution 2.40Å

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