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Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Kurkcuoglu Z, et al. Among authors: vangone a. J Comput Aided Mol Des. 2018 Jan;32(1):175-185. doi: 10.1007/s10822-017-0049-y. Epub 2017 Aug 22. J Comput Aided Mol Des. 2018. PMID: 28831657 Free PMC article.
Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.
Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Vangone A, et al. Proteins. 2017 Mar;85(3):417-423. doi: 10.1002/prot.25198. Epub 2016 Nov 24. Proteins. 2017. PMID: 27802573 Free PMC article.
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. Xue LC, et al. Among authors: vangone a. Bioinformatics. 2016 Dec 1;32(23):3676-3678. doi: 10.1093/bioinformatics/btw514. Epub 2016 Aug 8. Bioinformatics. 2016. PMID: 27503228
An important aspect of this is the ability to accurately predict the binding strength for a given protein-protein complex. Here we present PROtein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein-protein complexes from the …
An important aspect of this is the ability to accurately predict the binding strength for a given protein-protein complex. Here we pr …
An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.
Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira I, Kurkcuoglu Z, Vangone A, Bonvin AMJJ. Koukos PI, et al. Among authors: vangone a. Proteins. 2020 Aug;88(8):1029-1036. doi: 10.1002/prot.25869. Epub 2020 Jan 7. Proteins. 2020. PMID: 31886559
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes.
Vangone A, Bonvin AMJJ. Vangone A, et al. Bio Protoc. 2017 Feb 5;7(3):e2124. doi: 10.21769/BioProtoc.2124. eCollection 2017 Feb 5. Bio Protoc. 2017. PMID: 34458447 Free PMC article.
Many efforts have been devoted to unraveling principles of protein-protein interactions. Recently, we introduced a simple but robust descriptor of binding affinity based only on structural properties of a protein-protein complex. In Vangone and Bonvin (2015), …
Many efforts have been devoted to unraveling principles of protein-protein interactions. Recently, we introduced a simple but robust …
Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).
Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Vangone A, et al. Proteins. 2017 Aug;85(8):1589-1590. doi: 10.1002/prot.25339. Proteins. 2017. PMID: 28730688 Free PMC article. No abstract available.
32 results