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Items: 1 to 20 of 113

1.

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).

Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T.

Proteins. 2018 Mar;86 Suppl 1:27-50. doi: 10.1002/prot.25392. Epub 2017 Oct 16.

2.

Some of the most interesting CASP11 targets through the eyes of their authors.

Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T.

Proteins. 2016 Sep;84 Suppl 1:34-50. doi: 10.1002/prot.24942. Epub 2015 Nov 16.

3.

Assessment of the model refinement category in CASP12.

Hovan L, Oleinikovas V, Yalinca H, Kryshtafovych A, Saladino G, Gervasio FL.

Proteins. 2018 Mar;86 Suppl 1:152-167. doi: 10.1002/prot.25409. Epub 2017 Nov 29.

PMID:
29071750
4.

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age.

Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AMJJ.

Proteins. 2018 Mar;86 Suppl 1:51-66. doi: 10.1002/prot.25407. Epub 2017 Nov 7.

5.

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.

Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T.

Proteins. 2014 Feb;82 Suppl 2:26-42. doi: 10.1002/prot.24489. Erratum in: Proteins. 2015 Jun;83(6):1198.

6.

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods.

Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M.

Proteins. 2018 Mar;86 Suppl 1:97-112. doi: 10.1002/prot.25423. Epub 2017 Nov 29.

PMID:
29139163
7.

Protein structure prediction using Rosetta in CASP12.

Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D.

Proteins. 2018 Mar;86 Suppl 1:113-121. doi: 10.1002/prot.25390. Epub 2017 Oct 8.

PMID:
28940798
8.

Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Buchan DWA, Jones DT.

Proteins. 2018 Mar;86 Suppl 1:78-83. doi: 10.1002/prot.25379. Epub 2017 Sep 29.

9.

Assessment of protein assembly prediction in CASP12.

Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B, Duarte JM, Schwede T, Capitani G.

Proteins. 2018 Mar;86 Suppl 1:247-256. doi: 10.1002/prot.25408. Epub 2017 Nov 8.

10.

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K.

Proteins. 2018 Mar;86 Suppl 1:202-214. doi: 10.1002/prot.25452. Epub 2018 Feb 7.

11.

CASP6 data processing and automatic evaluation at the protein structure prediction center.

Kryshtafovych A, Milostan M, Szajkowski L, Daniluk P, Fidelis K.

Proteins. 2005;61 Suppl 7:19-23.

PMID:
16187343
12.

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.

Park H, Kim DE, Ovchinnikov S, Baker D, DiMaio F.

Proteins. 2018 Mar;86 Suppl 1:283-291. doi: 10.1002/prot.25387. Epub 2017 Oct 16.

13.

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

Adhikari B, Hou J, Cheng J.

Proteins. 2018 Mar;86 Suppl 1:84-96. doi: 10.1002/prot.25405. Epub 2017 Oct 31.

14.

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra A, Moult J, Phillips GN Jr, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T.

Proteins. 2019 Aug 23. doi: 10.1002/prot.25805. [Epub ahead of print]

PMID:
31442339
15.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

16.

Analysis of deep learning methods for blind protein contact prediction in CASP12.

Wang S, Sun S, Xu J.

Proteins. 2018 Mar;86 Suppl 1:67-77. doi: 10.1002/prot.25377. Epub 2017 Sep 6.

17.

Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.

Terashi G, Kihara D.

Proteins. 2018 Mar;86 Suppl 1:189-201. doi: 10.1002/prot.25373. Epub 2017 Sep 1.

18.

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.

Zhang C, Mortuza SM, He B, Wang Y, Zhang Y.

Proteins. 2018 Mar;86 Suppl 1:136-151. doi: 10.1002/prot.25414. Epub 2017 Nov 14.

19.

Critical assessment of methods of protein structure prediction (CASP)-Round XII.

Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A.

Proteins. 2018 Mar;86 Suppl 1:7-15. doi: 10.1002/prot.25415. Epub 2017 Dec 15.

20.

Data-assisted protein structure modeling by global optimization in CASP12.

Joo K, Heo S, Joung I, Hong SH, Lee SJ, Lee J.

Proteins. 2018 Mar;86 Suppl 1:240-246. doi: 10.1002/prot.25457. Epub 2018 Feb 1.

PMID:
29341255

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