Literature DB >> 11266167

Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions.

A Logean1, A Sette, D Rognan.   

Abstract

A tailor-made free energy scoring method (Fresno) has been compared to six universal scoring functions (Chemscore, Dock, FlexX, Gold, Pmf, Score) for predicting the binding affinity of 26 peptides to the class I human major histocompatibility protein HLA-B*2705. Fresno clearly outperforms all six universal scoring functions.

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Year:  2001        PMID： 11266167     DOI： 10.1016/s0960-894x(01)00021-x

Source DB:  PubMed          Journal:  Bioorg Med Chem Lett        ISSN： 0960-894X            Impact factor:   2.823


  11 in total

1.  Recovery of known T-cell epitopes by computational scanning of a viral genome.

Authors:  Antoine Logean; Didier Rognan
Journal:  J Comput Aided Mol Des       Date:  2002-04       Impact factor: 3.686

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Authors:  Isabella A Guedes; Camila S de Magalhães; Laurent E Dardenne
Journal:  Biophys Rev       Date:  2013-12-21

3.  Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation.

Authors:  Takeshi Ishikawa
Journal:  J Comput Aided Mol Des       Date:  2016-09-13       Impact factor: 3.686

4.  Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone.

Authors:  Irini A. Doytchinova; Paul Taylor; Darren R. Flower
Journal:  J Biomed Biotechnol       Date:  2003

5.  T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges.

Authors:  Matthew N Davies; Darren R Flower; Kanchan Phadwal; Isabel K Macdonald; Peter V Coveney; Shunzhou Wan
Journal:  Immunome Res       Date:  2010-11-03

Review 6.  Machine Learning Methods for Predicting HLA-Peptide Binding Activity.

Authors:  Heng Luo; Hao Ye; Hui Wen Ng; Leming Shi; Weida Tong; Donna L Mendrick; Huixiao Hong
Journal:  Bioinform Biol Insights       Date:  2015-10-11

Review 7.  Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges.

Authors:  Isabella A Guedes; Felipe S S Pereira; Laurent E Dardenne
Journal:  Front Pharmacol       Date:  2018-09-24       Impact factor: 5.810

8.  Modeling the adaptive immune system: predictions and simulations.

Authors:  Claus Lundegaard; Ole Lund; Can Kesmir; Søren Brunak; Morten Nielsen
Journal:  Bioinformatics       Date:  2007-11-28       Impact factor: 6.937

Review 9.  T-cell epitope vaccine design by immunoinformatics.

Authors:  Atanas Patronov; Irini Doytchinova
Journal:  Open Biol       Date:  2013-01-08       Impact factor: 6.411

10.  Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests.

Authors:  Jayvee R Abella; Dinler A Antunes; Cecilia Clementi; Lydia E Kavraki
Journal:  Front Immunol       Date:  2020-07-22       Impact factor: 7.561
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