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Assessing the accuracy of contact and distance predictions in CASP14.
Ruiz-Serra V, Pontes C, Milanetti E, Kryshtafovych A, Lepore R, Valencia A. Ruiz-Serra V, et al. Among authors: valencia a. Proteins. 2021 Dec;89(12):1888-1900. doi: 10.1002/prot.26248. Epub 2021 Oct 3. Proteins. 2021. PMID: 34595772 Free PMC article.
CASP6 assessment of contact prediction.
Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. Graña O, et al. Among authors: valencia a. Proteins. 2005;61 Suppl 7:214-224. doi: 10.1002/prot.20739. Proteins. 2005. PMID: 16187364
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: valencia a. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group.
De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. De Mattos-Arruda L, et al. Among authors: valencia a. Ann Oncol. 2020 Aug;31(8):978-990. doi: 10.1016/j.annonc.2020.05.008. Epub 2020 Jun 28. Ann Oncol. 2020. PMID: 32610166 Free PMC article.
The structural coverage of the human proteome before and after AlphaFold.
Porta-Pardo E, Ruiz-Serra V, Valentini S, Valencia A. Porta-Pardo E, et al. Among authors: valencia a. PLoS Comput Biol. 2022 Jan 24;18(1):e1009818. doi: 10.1371/journal.pcbi.1009818. eCollection 2022 Jan. PLoS Comput Biol. 2022. PMID: 35073311 Free PMC article.
957 results