AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains
| Autor: | Jake Parker, Jaime Prilusky, Gideon Lapidoth, Sarel J. Fleishman |
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| Rok vydání: | 2018 |
| Předmět: |
Models
Molecular Statistics and Probability Protein Conformation Interface (Java) Computer science Biochemistry Article Antibodies 03 medical and health sciences Protein structure Chain (algebraic topology) Sampling (signal processing) Molecular Biology 030304 developmental biology 0303 health sciences Computers Orientation (computer vision) 030302 biochemistry & molecular biology Computer Science Applications Computational Mathematics Variable (computer science) Sequence homology Computational Theory and Mathematics Monte Carlo Method Algorithm Software |
| Zdroj: | Bioinformatics. 35:1591-1593 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Summary Methods for antibody structure prediction rely on sequence homology to experimentally determined structures. Resulting models may be accurate but are often stereochemically strained, limiting their usefulness in modeling and design workflows. We present the AbPredict 2 web-server, which instead of using sequence homology, conducts a Monte Carlo-based search for low-energy combinations of backbone conformations to yield accurate and unstrained antibody structures. Availability and implementation We introduce several important improvements over the previous AbPredict implementation: (i) backbones and sidechains are now modeled using ideal bond lengths and angles, substantially reducing stereochemical strain, (ii) sampling of the rigid-body orientation at the light-heavy chain interface is improved, increasing model accuracy and (iii) runtime is reduced 20-fold without compromising accuracy, enabling the implementation of AbPredict 2 as a fully automated web-server (http://abpredict.weizmann.ac.il). Accurate and unstrained antibody model structures may in some cases obviate the need for experimental structures in antibody optimization workflows. |
| Databáze: | OpenAIRE |
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