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PEER-REVIEWED PAPERS / BOOK CHAPTERS

  1. Lawson CL, Kryshtafovych A, Pintilie GD, ..., Schmid M, Berman HM, Chiu W. (2024). Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Submitted to Nature Methods. doi:10.21203/rs.3.rs-3864137/v1. Epub 2024 Jan 25.
  2. Lee S, Kim G, Karin L, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. (2024). Petascale Homology Search for Structure Prediction. Cold Spring Harb Perspect Biol. 2024 Feb 5: a041465. doi: 10.1101/cshperspect.a041465. Online ahead of print. PMID: 38316555
  3. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. (2023). Critical assessment of methods of protein structure prediction (CASP)-Round XV. Proteins. 2023 Dec;91(12):1539-1549. doi: 10.1002/prot.26617. Epub 2023 Nov 2. PMID: 37920879
  4. Kryshtafovych A, Montelione G, Rigden D, Mesdaghi S, Karaca E, Moult J. (2023). Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins. 2023 Dec;91(12):1903-1911. doi: 10.1002/prot.26584. Epub 2023 Oct 23. PMID: 37872703
  5. Kryshtafovych A, Rigden DJ. (2023). To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units. Proteins. 2023 Dec;91(12):1558-1570. doi: 10.1002/prot.26533. Epub 2023 May 31. PMID: 37254889
  6. Simpkin AJ, Mesdaghi S, Sánchez Rodríguez F, Elliott L, Murphy DL, Kryshtafovych A, Keegan RM, Rigden DJ. (2023). Tertiary structure assessment at CASP15. Proteins. 2023 Dec;91(12):1616-1635. doi: 10.1002/prot.26593. Epub 2023 Sep 25. PMID: 37746927
  7. Ozden B, Kryshtafovych A, Karaca E. (2023). The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15. Proteins. 2023 Dec;91(12):1636-1657. doi: 10.1002/prot.26598. Epub 2023 Oct 20. PMID: 37861057
  8. Mulvaney T, Kretsch RC, Elliott L, Beton L, Kryshtafovych A, Rigden D, Das R, Topf M. (2023). CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. Proteins. 2023 Dec;91(12):1935-1951. doi: 10.1002/prot.26644. PMID: 37994556
  9. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN Jr, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. (2023). Proteins. 2023 Dec;91(12):1571-1599. doi: 10.1002/prot.26545. Epub 2023 Jul 26. PMID: 37493353
  10. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. (2023). RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins. 2023 Dec;91(12):1600-1615. doi: 10.1002/prot.26550. Epub 2023 Jul 19. PMID: 37466021
  11. Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, Fidelis K, Moult J. (2023). New prediction categories in CASP15. Proteins. 2023 Dec;91(12):1550-1557. doi: 10.1002/prot.26515. Epub 2023 Jun 12. PMID: 37306011
  12. Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill K, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung L-W, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastryrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Sarkar D, Schäfer LU, Schmidt MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wankowicz S, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. (2021). Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. 2021; 18:156-164. Published online: https://doi.org/10.1038/s41592-020-01051-w.
  13. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. (2021). Critical assessment of methods of protein structure prediction (CASP) - round XIV. Proteins. 2021; 89(12), 1607-1617. Published online: 2021 Sep 17. doi: 10.1002/prot.26237. PMID: 34533838
  14. Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovic K, Seok C, Venclovas C, Won J. (2021). Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins. 2021; 89(12), 1987-1996. Published online: 2021 Aug 30. doi: 10.1002/prot.26231. PMID: 34462960
  15. Kryshtafovych A, Moult J, Albrecht R, Chang GA, Chao K, Fraser A, Greenfield J, Hartmann MD, Herzberg O, Josts I, Leiman PG, Linden SB, Lupas AN, Nelson DC, Rees SD, Shang X, Sokolova ML, Tidow H, AlphaFold2 team. (2021). Computational models in the service of X-ray and cryo-EM structure determination. Proteins. 2021; 89(12), 1633-1646. Published online: 2021 Aug 27. doi: 10.1002/prot.26223. PMID: 34449113
  16. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. (2021). Target highlights in CASP14: analysis of models by structure providers. Proteins. 2021; 89(12), 1647-1672. Published online: 2021 Sep 25. doi: 10.1002/prot.26247. PMID: 34561912
  17. Ozden B, Kryshtafovych A, Karaca E. (2021). Assessment of the CASP14 Assembly Predictions. Proteins. 2021; 89(12), 1787-1799. Published online: 2021 Aug 1. doi: 10.1002/prot.26199. PMID: 34337786
  18. Cragnolini T, Kryshtafovych A, Topf M. (2021). Cryo-EM targets in CASP14. Proteins. 2021; 89(12), 1949-1958. Published online: 2021 Aug 16. doi: 10.1002/prot.26216. PMID: 34398978
  19. Simpkin AJ, Sánchez Rodríguez F, Mesdaghi S, Kryshtafovych A, Rigden DJ. (2021). Evaluation of model refinement in CASP14. Proteins. 2021; 89(12), 1852-1869. Published online: 2021 Jul 20. doi: 10.1002/prot.26185. PMID: 34288138
  20. Kinch LN, Schaeffer RD, Kryshtafovych A, Grishin NV. (2021). Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14). Proteins. 2021; 89(12), 1618-1632. Published online: 2021 Aug 4. doi: 10.1002/prot.26202. PMID: 34350630
  21. Kinch LN, Pei J, Kryshtafovych A, Schaeffer RD, Grishin NV. (2021). Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction. Proteins. 2021; 89(12), 1673-1686. Published online: 2021 Jul 9. doi: 10.1002/prot.26172. PMID: 34240477
  22. Kwon S, Won J, Kryshtafovych A, Seok C. (2021). Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges. Proteins. 2021; 89(12), 1940-1948. Published online: 2021 Jul 29. doi: 10.1002/prot.26192. PMID: 34324227
  23. Huang YJ, Zhang N, Bersch B, Fidelis K, Inouye M, Ishida Y, Kryshtafovych A, Kobayashi N, Kuroda Y, Liu G, LiWang A, Swapna GVT, Wu N, Yamazaki T, Montelione GT. (2021). Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2. Proteins. 2021; 89(12), 1959-1976. Published online: 2021 Sep 24. doi: 10.1002/prot.26246. PMID: 34559429
  24. Ruiz-Serra V, Pontes C, Milanetti E, Kryshtafovych A, Lepore R, Valencia A. (2021). Assessing the accuracy of contact and distance predictions in CASP14. Proteins. 2021; 89(12), 1888-1900. Published online: 2021 Oct 3. doi: 10.1002/prot.26246. PMID: 34595772
  25. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. (2019). Critical assessment of methods of protein structure prediction (CASP) - round XIII. Proteins. 2019; 87 (12), 1011-1020. Published online: 2019 Oct 7. doi: 10.1002/prot.25823. PMID:31589781
  26. Kinch LN, Kryshtafovych A, Monastyrskyy B, Grishin N. (2019). CASP13 target classification into tertiary structure prediction categories. Proteins. 2019; 87 (12), 1021-1036. Published online: 2019 Jul 11. doi: 10.1002/prot.25775. PMID:31294862
  27. Kryshtafovych A, Malhotra S, Monastyrskyy B, Cragnolini T, Joseph A-P, Chiu W., Topf M. (2019). Cryo-EM targets in CASP13: overview and evaluation results. Proteins. 2019; 87 (12), 1128-1140. Published online: 2019 Oct 1. doi: 10.1002/prot.25817. PMID:31576602
  28. JE Fajardo, R Shrestha, N Gil, A Belsom, SN Crivelli, C Czaplewski, K Fidelis, S Grudinin, M Karasikov, AS Karczynska, A Kryshtafovych, A Leitner, A Liwo, EA Lubecka, B Monastyrskyy, G Pagčs, Juri Rappsilber, AK Sieradzan, C Sikorska, E Trabjerg, A Fiser. (2019). Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins. 2019; 87 (12), 1283-1297. Published online: 2019 Sep 30. doi: 10.1002/prot.25816. PMID:31569265
  29. Shrestha R, Fajardo E, Gil N, Fidelis K, Kryshtafovych A, Monastyrskyy B, Fiser A. (2019). Assessing the accuracy of contact predictions in CASP13. Proteins. 2019; 87 (12), 1058-1068. Published online: 2019 Oct 6. doi: 10.1002/prot.25819. PMID:31587357
  30. Guzenko D, Lafita A, Monastyrskyy B, Kryshtafovych A, Duarte JM. (2019). Assessment of protein assembly prediction in CASP13. Proteins. 2019; 87 (12), 1190-1199. Published online: 2019 Aug 2. doi: 10.1002/prot.25795. PMID:31374138
  31. Read RJ, Sammito MD, Kryshtafovych A, Croll TI. (2019). Evaluation of model refinement in CASP13. Proteins. 2019; 87 (12), 1249-1262. Published online: 2019 Jul 31. doi: 10.1002/prot.25794. [Epub ahead of print]. PMID:31365160
  32. 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. (2019). Target highlights in CASP13: experimental target structures through the eyes of their authors. Proteins. 2019; 87 (12), 1037-1057. Published online: 2019 Aug 23. doi: 10.1002/prot.25805. PMID: 31442339
  33. Croll TI, Sammito MD, Kryshtafovych A, Read RJ. (2019). Evaluation of template-based modeling in CASP13. Proteins. 2019; 87 (12), 1113-1127. Published online: 2019 Aug 13. doi: 10.1002/prot.25800. PMID:31407380
  34. Won J, Baek M, Monastyrskyy B, Kryshtafovych A, Seok C. (2019). Assessment of Protein Model Structure Accuracy Estimation in CASP13: Challenges in the Era of Deep Learning. Proteins. 2019; 87 (12), 1351-1360. Published online: 2019 Aug 22. doi: 10.1002/prot.25804. PMID:31436360
  35. Sala D, Huang YJ, Cole CA, Snyder D, Liu G, Ishida Y, Swapna G.V.T., Fidelis K, Kryshtafovych A, Inouye M, Tejero R, Valafar H, Rosato A, Montelione GT. (2019). Protein structure prediction assisted with sparse NMR data in CASP13. Proteins. 2019; 87 (12), 1315-1332. Published online: 2019 Oct 11. doi: 10.1002/prot.25837. PMID:31603581
  36. Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. (2019). Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins. 2019; 87 (12), 1298-1314. Published online: 2019 Oct 7. doi: 10.1002/prot.25827. PMID:31589784
  37. Olechnovic K, Monastyrskyy B, Kryshtafovych A, Venclovas C. (2019). Comparative analysis of methods for evaluation of protein models against native structures. Bioinformatics. 2019; 35(6), 937-944. doi: 10.1093/bioinformatics/bty760. PMID:30169622
  38. Kryshtafovych A, Adams PD, Lawson CL, Chiu W. (2018). Evaluation system and web infrastructure for the second cryo-EM model challenge. J Struct Biol. 2018; 204, 96-108. doi: 10.1016/j.jsb.2018.07.006. PMID:30017700
  39. Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W. (2018). Distribution of evaluation scores for models submitted to the second cryo-EM model challenge. Data in Brief. 20, 1629-1638. doi: 10.1016/j.dib.2018.08.214. PMID:30263915
  40. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. (2018). Critical assessment of methods of protein structure prediction (CASP) - round XII. Proteins. 2018; 86 (S1), 7-15. doi: 10.1002/prot.25415. PMID:29082672
  41. Abriata LA, Kinch LN, Tamň GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. (2018). Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics. Proteins. 2018; 86 (S1), 16-26. doi: 10.1002/prot.25403. PMID: 29044714
  42. Kryshtafovych A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. (2018). Assessment of model accuracy estimations in CASP12. Proteins. 2018; 86 (S1), 345-360. doi: 10.1002/prot.25371. PMID: 28833563
  43. Kryshtafovych A, Monastyrskyy B, Fidelis K, Moult J, Schwede T, Tramontano A. (2018). Evaluation of the template-based modeling in CASP12. Proteins. 2018; 86 (S1), 321-334. doi: 10.1002/prot.25425. PMID: 29159950
  44. Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AMJJ. (2018). Assessment of Contact Predictions in CASP12: Co-Evolution and Deep Learning Coming of Age. Proteins. 2018; 86 (S1), 51-66. doi: 10.1002/prot.25407. PMID: 29071738
  45. Abriata LA, Tamň GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. (2018). Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins. 2018; 86 (S1), 97-112. doi: 10.1002/prot.25423. PMID: 29139163
  46. Hovan L, Oleinikovas V, Yalinca H, Kryshtafovych A, Saladino G, Gervasio FL. (2018). Assessment of the model refinement category in CASP12. Proteins. 2018; 86 (S1), 152-167. doi: 10.1002/prot.25409. PMID: 29071750
  47. Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B, Duarte JM, Schwede T, Capitani G. (2018). Assessment of protein assembly prediction in CASP12. Proteins. 2018; 86 (S1), 247-256. doi: 10.1002/prot.25408. PMID: 29071742
  48. 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. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins. 2018; 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 28960539
  49. Moult J, Fidelis K, Kryshtafovych A, Schwede T. (2018). A tribute to Anna Tramontano (1957 - 2017). Proteins. 2018; 86 (S1), 5-6. doi: 10.1002/prot.25406. PMID: 29067782
  50. Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K. (2018). Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy. Proteins. 2018; 86 (S1), 202-214. doi: 10.1002/prot.25452. PMID: 29067782
  51. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. (2016). Critical assessment of methods of protein structure prediction (CASP) - progress and new directions in round XI. Proteins. 2016; 84 (S1), 4-14. Published online: doi: 10.1002/prot.25064. PMID: 27171127
  52. Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. (2016). Assessment of CASP11 Contact-Assisted Predictions. Proteins. 2016; 84 (S1), 164-180. Published online: doi: 10.1002/prot.25020. PMID: 26889875
  53. Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV. (2016). CASP 11 Target Classification. Proteins. 2016; 84 (S1), 20-33. Published online: doi: 10.1002/prot.24982. PMID: 26756794
  54. Kryshtafovych A, Monastyrskyy B, Fidelis K. (2016). CASP11 statistics and the prediction center evaluation system. Proteins. 2016; 84 (S1), 15-19. Published online: doi: 10.1002/prot.25005. PMID: 26857434
  55. Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. (2016). Evaluation of free modeling targets in CASP11 and ROLL. Proteins. 2016; 84 (S1), 51-66. Published online: doi: 10.1002/prot.24973. PMID: 26677002
  56. Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. (2016). New encouraging developments in contact prediction: Assessment of the CASP11 results. Proteins. 2016; 84 (S1), 131-144. Published online: doi: 10.1002/prot.24943. PMID: 26474083
  57. Kryshtafovych A, Barbato A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. (2016). Methods of model accuracy setimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11. Proteins. 2016; 84 (S1), 349-369. Published online: doi: 10.1002/prot.24919. PMID: 26344049
  58. 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. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins. 2016; 84 (S1), 34-50. Published onlilne: doi: 10.1002/prot.24942. PMID: 26473983
  59. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. (2014). Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins. 2014; 82 (S2), 1-6. Published online: DOI 10.1002/prot.24452.
  60. Taylor T, Tai C-H, Huang YJ, Block J, Bai H, Kryshtafovych A, Montelione GT, Lee BK. (2014). Definition and classification of evaluation units for CASP10. Proteins. 2014; 82 (S2), 14-25. Published online: doi: 10.1002/prot.24434.
  61. Kryshtafovych A, Barbato A, Fidelis K, Monastyrskyy B, Schwede T, Tramontano A. (2014). Assessment of the assessment: Evaluation of the model quality estimates in CASP10. Proteins. 2014; 82 (S2), 112-126. Published online: doi: 10.1002/prot.24347.
  62. Monastyrskyy B, Kryshtafovych A, Moult J, Tramontano A, Fidelis K. (2014). Assessment of protein disorder region predictions in CASP10. Proteins. 2014; 82 (S2), 127-137. Published online: DOI 10.1002/prot.24391.
  63. Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. (2014). Evaluation of residue-residue contact predictions in CASP10. Proteins. 2014; 82 (S2), 138-153. Published online: DOI 10.1002/prot.24340.
  64. Kryshtafovych A, Fidelis K, Moult J. (2014). CASP10 results compared to those of previous CASP experiments. Proteins. 2014; 82 (S2), 164-174. Published online: DOI 10.1002/prot.24448.
  65. Kryshtafovych A, Monastyrskyy B, Fidelis K. (2014). CASP Prediction Center infrastructure and evaluation measures in CASP10 and CASP ROLL. Proteins. 2014; 82 (S2), 7-13. Published online: DOI 10.1002/prot.24399.
  66. 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. (2014). 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. Proteins. 2014; 82 (S2), 26-42. Published online: DOI 10.1002/prot.24489. PMID: 24318984.
  67. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. (2011). Critical assessment of methods of protein structure prediction (CASP) - round IX. Proteins. 2011; 79 (S10), 1-5. Published online: DOI 10.1002/prot.23200.
  68. Kryshtafovych A, Fidelis K, Tramontano A. (2011). Evaluation of model quality predictions in CASP9. Proteins. 2011; 79 (S10), 91-106. Published online: DOI 10.1002/prot.23180.
  69. Monastyrskyy B, Fidelis K, Moult J, Tramontano A, Kryshtafovych A. (2011). Evaluation of disorder predictions in CASP9. Proteins. 2011; 79 (S10), 107-118. Published online: DOI 10.1002/prot.23161.
  70. Monastyrskyy B, Fidelis K, Tramontano A, Kryshtafovych A. (2011). Evaluation of residue-residue contact predictions in CASP9. Proteins. 2011; 79 (S10), 119-125. Published online: DOI 10.1002/prot.23160.
  71. Kryshtafovych A, Fidelis K, Moult J. (2011). CASP9 results compared to those of previous CASP experiments. Proteins. 2011; 79 (S10), 196-207. Published online: DOI 10.1002/prot.23182.
  72. Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Jayaraman S, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins. 2011; 79 (S10), 6-20. Published online: DOI 10.1002/prot.23196.
  73. Kryshtafovych A, Fidelis K, Moult J. (2010). CASP: a driving force in protein structure modeling. A book chapter in: Introduction to Protein Structure Modeling: Methods and Algorithms (edited by H.Rangwala and G.Karypis), 15-32. Published online: DOI 10.1002/9780470882207.ch2
  74. Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A. (2009). Critical assessment of methods of protein structure prediction (CASP) - round VIII. Proteins. 2009; 77 (Suppl 9), 1-4.
  75. Kryshtafovych A, Krysko O, Daniluk P, Dmytriv Z, Fidelis K. (2009). Protein structure prediction center in CASP8. Proteins. 2009; 77 (Suppl 9), 5-9.
  76. Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. (2009). Evaluation of template-based models in CASP8 with standard measures. Proteins. 2009; 77 (Suppl 9), 18-28.
  77. Cozzetto D, Kryshtafovych A, Tramontano A. (2009). Evaluation of CASP8 model quality predictions. Proteins. 2009; 77 (Suppl 9), 157-166.
  78. Kryshtafovych A, Fidelis K, Moult J. (2009). CASP8 results in context of previous experiments. Proteins 77 (Suppl 9), 217-228.
  79. Hvidsten TR, Legreid A, Kryshtafovych A, Andersson G, Fidelis K, Komorowski J. (2009). A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PLoS One. 2009; 4(7), e6266.
  80. Bjorkholm, P., Daniluk, P., Kryshtafovych, A., Fidelis, K., Andersson, R., Hvidsten, TR. (2009). Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics. 2009; 25, 1264-1270.
  81. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H. M., Jones, D., Brenner, S. E., Burley, S. K., Das, R., Dokholyan, N. V., Dunbrack, R. L., Jr., Fidelis, K., Fiser, A., Godzik, A., Huang, Y. J., Humblet, C., Jacobson, M. P., Joachimiak, A., Krystek, S. R., Jr., Kortemme, T., Kryshtafovych, A., Montelione, G. T., Moult, J., Murray, D., Sanchez, R., Sosnick, T. R., Standley, D. M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J. D. & Wilson, I. A. (2009). Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure. 2009; 17, 151-159.
  82. Kryshtafovych, A. & Fidelis, K. (2009). Protein structure prediction and model quality assessment. Drug Discov Today. 2009; 14 (7/8), 386-393.
  83. Hvidsten, T.R., Kryshtafovych, A. & Fidelis, K. (2009). Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Proteins. 2009; 75(4), 870-884.
  84. Strombergsson, H., Daniluk, P., Kryshtafovych, A., Fidelis, K., Wikberg, J.E., Kleywegt, G.J. & Hvidsten, T.R. (2008). Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space. J Chem Inf Model. 2008; 48 (11), 2278-2288.
  85. Moult, J., Fidelis, K., Hubbard, T., Kryshtafovych, A., Rost, B. & Tramontano, A. (2007). Critical assessment of methods of protein structure prediction (CASP) - round 7. Proteins. 2007; 69 (S8), 3-9.
  86. Kryshtafovych, A., Fidelis, K. & Moult, J. (2007). Progress from CASP6 to CASP7. Proteins. 2007; 69 (S8), 194-207.
  87. Cozetto, D., Kryshtafovych, A., Ceriani, M. & Tramontano, A. (2007). Assessment of predictions in the Model Quality Assessment category. Proteins. 2007; 69 (S8), 175-183.
  88. Kryshtafovych, A., Prlic, A., Dmytriv, Z., Daniluk P., Milostan, M., Eyrich V., Hubbard, T. & Fidelis, K. (2007). New tools and expanded data analysis capabilities at the protein structure prediction center. Proteins. 2007; 69(S8), 19-26.
  89. Wilczynski, B., Hvidsten, T. R., Kryshtafovych, A., Tiuryn, J., Komorowski, J., Fidelis, K. (2006). Using local gene expression similarities to discover regulatory binding site modules. BMC Bioinformatics. 2006; 7, 505.
  90. Strombergsson, H., Kryshtafovych, A., Prusis, P., Fidelis, K., Wikberg, J., Komorowski, J. & Hvidsten, T. R. (2006). Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins. 2006; 65 (3), 568-579.
  91. Hvidsten, T. R., Wilczynski, B., Kryshtafovych, A., Tiuryn, J., Komorowski, J. & Fidelis, K. (2005). Discovering regulatory binding-site modules using rule-based learning. Genome Res. 2005; 15, 856-866.
  92. Kryshtafovych, A., Venclovas, C., Fidelis, K. & Moult, J. (2005). Progress over the first decade of CASP experiments. Proteins. 2005; 61 (S7), 225-236.
  93. Kryshtafovych, A., Milostan, M., Szajkowski, L., Daniluk, P. & Fidelis, K. (2005). CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins. 2005; 61 (S7), 19-23.
  94. Eyrich, V. A., Kryshtafovych, A., Milostan, M. & Fidelis, K. (2005). System for accepting server predictions in CASP6. Proteins. 2005; 61 (S7), 24-26.
  95. Hvidsten, T. R., Kryshtafovych, A., Komorowski, J. & Fidelis, K. (2003). A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics. 2003; 19 (S2), II81-II91.
  96. Kryshtafovych, A., Hvidsten, T.R., Komorowski, J. and Fidelis, K. (2003). Fold recognition using sequence fingerprints of protein local substructures. Proceedings of the IEEE Computational Systems Bioinformatics, Stanford, CA, August, 2003, 517-519.*
  97. Wilczynski, B., Hvidsten, T. R., Kryshtafovych, A., Stubbs, L., Komorowski, J. & Fidelis, K. (2003). A rule-based framework for gene regulation pathways discovery. Proceedings of the IEEE Computational Systems Bioinformatics, Stanford, CA, August 2003, 435-436.*
  98. Kryshtafovych, A.A. & Matysiak, S.J. (2001). Frictional contact of laminated elastic half-spaces allowing interface cavities. Part 1: Analytical treatment. International Journal for Numerical and Analytical Methods in Geomechanics 25 (11), 1077-1088.
  99. Kryshtafovych, A.A. & Matysiak, S.J. (2001). Frictional contact of laminated elastic half-spaces allowing interface cavities. Part 2: Numerical results. International Journal for Numerical and Analytical Methods in Geomechanics 25 (11), 1089-1099.
  100. Kryshtafovych, A. & Martynyak, R. (2001). Strength of a system of mated anisotropic half-planes with locally uneven boundaries. International Journal of Engineering Science 39, 403-413.
  101. Martynyak, R.M. & Kryshtafovych, A.A. (2000). Frictional contact between two elastic semiplanes with local surface depressions. Friction and Wear 21 (4), 350-360.
  102. Kryshtafovych A.A. & Martynyak R.M. (2000). Frictional contact between two elastic semiplanes with wavy surfaces. Friction and Wear 21 (5), 465-473.
  103. Kit, H.S., Martynyak, R.M., Kryshtafovych, A.A. & Machyshyn, I.M. (2000). Friction effect on the parameters of thermal and diffusion contact of elastic bodies with regular profile. Mashynoznavstvo 3, 3-8.
  104. Kryshtafovych, A.A. & Martynyak, R.M. (1999). Lamination of anisotropic half-spaces in the presence of contact thermal resistance. International Applied Mechanics 35 (2), 159-164.
  105. Kryshtafovych, A. & Shvets, R. (1999). On strength of anisotropic half-plane with wavy boundary compressed versus isotropic half-plane. In book "Fracture Mechanics of Materials and Structural Integrity", 2nd edition: (in 3 volumes, edited by V.V.Panasiuk)- Lviv: Kameniar, 1999.- Vol. 2.- 295-298.
  106. Martynyak, R.M., Kryshtafovych, A.A., & Machyshyn, I.M. (1999). Unilateral contact of bodies with conforming surfaces under an action of heat sources and sinks. Proceedings of I.Franko Lviv University 55, 169-173.
  107. Matczynski, M., Martynyak, R. and Kryshtafovych, A. (1999). Contact problem of a crack filled with heat-conducting gas. Proceedings of the 3rd International Symposium on Thermal Stresses, Cracow, Poland, June 13-17, 1999.- In book Thermal Stresses '99 (edited by J.J.Skrzypek and R.B.Hetnarski), 127-130.*
  108. Shvets, R., Kryshtafovych, A., and Martynyak, R. (1999). Method of singular integro-differential equations in the problems on imperfect thermoelastic contact of anisotropic bodies. Proceedings of the 3rd International Symposium on Thermal Stresses, Cracow, Poland, June 13-17, 1999.- In book Thermal Stresses '99 (edited by J.J.Skrzypek and R.B.Hetnarski), 131-134.*
  109. Kryshtafovych, A.A. & Martynyak, R.M. (1998). On the contact interaction of dissimilar anisotropic half-planes with thermally insulated gaps at the interface. Journal of Mathematical Sciences 88 (3), 425-431.
  110. Kryshtafovych, A.A. (1998). Influence of surface defects of a rigid base on the strength of a pressed anisotropic body. Materials Science 34 (1), 128-132.
  111. Kit, H., Martynyak, R. & Kryshtafovych, A. (1998). Growth of plastic zones due to heat loading near a closed interface crack. Journal of Theoretical and Applied Mechanics 36 (2), 249-260.
  112. Kryshtafovych, A.A. & Martynyak, R.M. (1998). Thermoelastic contact of anisotropic half-spaces with thermal resistance. International Applied Mechanics 34 (7), 629-634.
  113. Kryshtafovych, A.A., Martynyak, R.M. & Shvets, R.M. (1998). Analysis of failure loadings at contact of anisotropic and isotropic half-planes with local surface recess-type flaws. In book Fracture from Defects (in 3 volumes, editors M.W.Brown, E.R. de los Rios and K.J.Miller).- Vol. 2, 1011-1016.
  114. Shvets, R., Martynyak, R., and Kryshtafovych, A. (1997). Thermoelastic Interaction of Anisotropic Half-Planes with Disturbed Surfaces. Proceedings of the 2nd International Symposium on Thermal Stresses and Related Topics «Thermal Stresses '97», Rochester, U.S.A., June 8-11, 1997, 509-512.*
  115. Kryshtafovych, A.A. (1996). The influence of Frictional Forces on the Interaction between an Anisotropic Half-Plane and an Absolutely Rigid Body with a Cavity in Its Surface. Journal of Mathematical Sciences 81 (6), 3084-3089.
  116. Shvets, R.M., Martynyak, R.M. & Kryshtafovych, A.A. (1996). Discontinuous contact of an anisotropic half-plane and a rigid base with disturbed surface. International Journal of Engineering Science 34 (2), 183-200.
  117. Kryshtafovych, A.A., Martynyak, R.M. & Shvets, R.M. (1994). Contact Interaction of Anisotropic Half-Plane and a Rigid Body Having Regular Surface Microtopography. Friction and Wear 15 (3), 366.
  118. Martynyak, R.M & Kryshtafovych, A.A. (1994). Contact problem for an Anisotropic Half-Plane and a Rigid Body with Uneven Surface. International Applied Mechanics 30 (7), 539-543.
  119. Kryshtafovych, A.A. (1994). Conditions of Heat Contact of Anisotropic Bodies Via a Thin Anisotropic Layer. Materials Science 30 (6), 699-701.
  120. Martynyak, R., Kryshtafovych, A., and Shvets, R. (1993). The mathematical modelling of interaction and deformation of inhomogeneous anisotropic systems. Proc. Intern. AMSE Conference Applied Modelling & Simulation, Lviv, Ukraine, Sept.30-Oct.2, 1993, published by AMSE Press, 223-230.*
  121. Shvets, R.M., Martynyak, R.M. & Kryshtafovych, A.A. (1990). Incomplete mechanical contact between two elastic half-planes made of orthotropic materials. Soviet Materials Science 26 (3), 305-310.

    INVENTIONS /PATENTS

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  122. Fidelis, K. and Kryshtafovych, A. (2003). Local Descriptors of Protein Structure. Patent IL-10728. FreshPatents.com, p. 40, USA.

    OTHER PUBLICATIONS (proceedings, conference abstracts, reports)

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  123. Huang, YJ., Zhang, N., Bersch, B., Fidelis, K., Inouye, M., Ishida, Y., Kryshtafovych, A., Kobayashi, N., Kuroda, Y., Liu, G., LiWang, A., Swapna, GVT., Wu, N., Yamazaki, T., Montelione, GT. (2022). Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2. Biophysical journal 121 (3); 45a; February 2022.
  124. Lawson, CL., Kryshtafovych, A., Pintilie, G., Berman, HM., Schmid, M., Chiu W. EMDataResource Ligand Model Challenge. BPS 2022. San Francisco, CA, USA; February 2022.
  125. Lawson, CL., Kryshtafovych, A., Adams, PD., Afonine, PV., Baker, ML., Barad, BA., Bond, P., Burnley, T., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K., Dill, K., DiMaio, F., Farrell, DP., Fraser, JS., Herzik, MA Jr., Hoh, SW., Hou, J., Hung, L-W., Igaev, M., Joseph, AP., Kihara, D., Kumar, D., Mittal, S., Monastryrskyy, B., Olek, M., Palmer, CM., Patwardhan, A., Perez, A., Pfab, J., Pintilie, GD., Richardson, JS., Sarkar, D., Schäfer, LU., Schmidt, MF., Schröder, GF., Shekhar, M., Si, D., Singharoy, A., Terashi, G., Terwilliger, TC., Vaiana, A., Wang, L., Wankowicz, S., Williams, CJ., Winn, M., Wu, T., Yu, X., Zhang, K., Berman, HM., Chiu, W. (2020). Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution. bioRxiv 2020.06.12.147033. doi: 10.1101/2020.06.12.147033.
  126. Lawson, CL., Kryshtafovych, A., Adams, PD., Afonine, PV., Baker, ML., Barad, BA., Bond, P., Burnley, T., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K., Dill, K., DiMaio, F., Farrell, DP., Fraser, JS., Herzik, MA Jr., Hoh, SW., Hou, J., Hung, L-W., Igaev, M., Joseph, AP., Kihara, D., Kumar, D., Mittal, S., Monastryrskyy, B., Olek, M., Palmer, CM., Patwardhan, A., Perez, A., Pfab, J., Pintilie, GD., Richardson, JS., Sarkar, D., Schäfer, LU., Schmidt, MF., Schröder, GF., Shekhar, M., Si, D., Singharoy, A., Terashi, G., Terwilliger, TC., Vaiana, A., Wang, L., Wankowicz, S., Williams, CJ., Winn, M., Wu, T., Yu, X., Zhang, K., Berman, HM., Chiu, W. (2020). 2019 EMDataResource Model Metrics Challenge Dataset. Zenodo. doi:10.5281/zenodo.4148789.
  127. Kryshtafovych, A., Lawson, CL., Chiu, W. (2020) 2019 cryo-EM model metrics challenge. 45th Lorne Conference on protein structure & function. Lorne, Australia, February 2020.
  128. Tai, C-H., Ishida, Y., Hura, G., Tsutakawa, S., Tainer, J., Kryshtafovych, A., Moult, J., Fidelis, K., Montelione, G. (2019). CASP_COMMONS: A Community Wide Program in Data Guided Protein Structure Prediction. ISMB/ECCB 2019, Basel, Switzerland, July 2019.
  129. Lawson, CL., Kryshtafovych, A., Pintilie, G., Berman, HM., Chiu, W. (2019). Outcomes of the cryo-EM map and model challenges. Biophysical Journal 116 (3), 160a.
  130. Kryshtafovych, A., Lawson, CL., Chiu, W. (2018). Evaluation of models in the 2016 cryo-EM model challenge. American Crystallographic Association 2018 Meeting, Toronto, Canada, July 2018, acaonline.secure-platform.com/a/gallery/rounds/1/details/236.
  131. Lawson, CL., Kryshtafovych, A., Chiu, W., Adams, PD., Brünger, A., Kleywegt, G., Patwardhan, A., Read, R., Schwede, T., Topf, M., Afonine, P., Avaylon, J., Baker, M., Braun, T., Cao, W., Chittori, S., Croll, T., DiMaio, F., Frenz, B., Grudinin, S., Hoffmann, A., Hryc, C., Joseph, AP., Kawabata, T., Kihara, D., Mao, Matthies, D., McGreevy, R., Nakamura, H., Nakamura, S., Nguyen, L., Schroeder, G., Shekhar, M., Shimizu, K., Singharoy, A., Sobolev, O., Tajkhorshid, E., Teo, I., Terashi, G., Terwilliger, T., Wang, K., Yu, I., Zhou, H., Sala, R. (2018). CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge. Zotero. doi:10.5281/zenodo.1165999.
  132. Kryshtafovych, A., Lawson, CL., Chiu, W. (2018). Evaluation of models in the 2016 cryo-EM model challenge. Foundations of Crystallography 74, a123.
  133. Ogorzalek, TL., Hura, GL., Kryshtafovych, A., Tainer, JA., Fidelis, K., Tsutakawa SE. (2018). Small angle X-ray scattering for data assisted structure prediction in CASP 12 with prospects to improve accuracy. BPS 62nd annual meeting, San Francisco, USA, February 2018. Biophysical Journal 114 (3), Suppl. 1, p.576a-577a. doi: 10.1016/j.bpj2017.11.3152
  134. Schaarschmidt, J., Monastyrskyy, B., Kryshtafovych, A., Bonvin AMJJ. (2018). Cover Image. Proteins 86(S1), C1-C1.
  135. Kryshtafovych, A. (2017). Template-based modeling: an awakened sleeping giant. 4th International Conference on Protein and RNA Structure Prediction Conference, Montego Bay, Jamaica, December 2017, p.10.
  136. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. (2016). Cover Image. Proteins 84(S1), C4-C4.
  137. Kryshtafovych, A. (2015). What do we need? Progress. When do we need it? Now. Contacts, accuracy estimates, and other exciting developments in protein modeling as evidenced by the CASP11 experiment. 3rd International Conference on Protein and RNA Structure Prediction Conference, Punta Cana, Dominical Republic, December 2015, p.6.
  138. Kryshtafovych, A. (2013). New developments in the assessment of contact predictions in CASP, and how to quantify improvements in model accuracy due to incorporation of contact information. 2nd Zing Protein and RNA Structure Prediction Conference, Playa del Carmen, Mexico, December 2013, p.38.
  139. Lukasiak, P., Wojciechowski, M., Ratajczak, T., Hasinski, K., Monastyrskyy, B., Kryshtafovych, A., Fidelis., K. (2012). Sphere Grinder - estimating similarity of structures on a local scale. CASP10, Gaeta, Italy, December 2012, p.274-275.
  140. Kryshtafovych, A., Monastyrskyy, B. & Fidelis K. (2012). Davis-QAconsensus / Davis-QAconsensusALL - the baseline quality assessment methods. CASP10, Gaeta, Italy, December 2012, p.273.
  141. Kryshtafovych, A.(2011). Model quality assessment in CASP: present and plans for the future. Zing Protein and RNA Structure Prediction Conference, Playa del Carmen, Mexico, December 2011, p.6.
  142. Antczak M., Lukasiak, P., Fidelis, K., Kryshtafovych, A., & Blazewicz, J. (2011). Protein structure quality assessment and modeling support techniques. Machine Learning Reports. ICOLE 2011, Lessach, Austria, September 2011, p.21-26.
  143. Bjorkholm, P., Lysholm, F., Kryshtafovych, A., Fidelis, K. & Hvidsten, TR. (2010). FragHMMent - contact prediction using hidden Markov models trained on alignments of local descriptors of protein structure. CASP 9, Pacific Grove, CA, USA, December 2010, p.98-99.
  144. Lukasiak, P., Fidelis, K., Antczak M., Kryshtafovych, A., & Blazewicz, J. (2010). Automated prediction of 3D structure proteins based on descriptors approach. Machine Learning Reports. ICOLE 2010, Lessach, Austria, September 2010, p.19-25.
  145. Bjorkholm, P., Daniluk, P., Kryshtafovych, A., Fidelis, K., Andersson, R. & Hvidsten, T. (2008). Predicting residue-residue contacts using hidden Markov models trained on local neighborhoods of protein structure. CASP 8, Cagliari, Italy, December 2008, p.54-55.
  146. Prlic, A., Kryshtafovych, A., Milostan, M., Dmytriv, Z., Fidelis, K. & Hubbard, T. (2008). Spice - a 3D viewer for CASP results. CASP 7.5, Madrid, Spain, April 2008.
  147. Strömbergsson, H., Hvidsten, T.R., Wikberg, J.E.S., Kryshtafovych, A., Daniluk, P., Fidelis, K. & Kleywegt, G.J. (2007). Enzyme wide modeling of protein-ligand interactions. ISMB, Vienna, Austria, July 2007.
  148. Hvidsten, T. R., Kryshtafovych, A., Daniluk, P., Fidelis, K. & Komorowski, J. (2006). Prediction of protein function using local descriptors of protein structure. CASP 7, Pacific Grove, CA, USA, November 2006, p.78-79.
  149. Hvidsten, T. R., Wilczynski, B., Kryshtafovych, A., Tiuryn J., Komorowski, J. & Fidelis, K. (2006). Learning regulatory binding site modules from sequence and expression data. RECOMB, Venice, Italy, April 2006.
  150. Hvidsten, T. R., Kryshtafovych, A., Daniluk P., Fidelis, K. & Komorowski, J. (2006). Prediction function from local substructures of proteins. 5th Swedish Bioinformatics workshop, p.18.
  151. Drabikowski, M., Fidelis, K., Kryshtafovych, A. & Tiuryn, J. (2005). Local descriptors library models the core of protein structure accurately. RECOMB, Cambridge, MA, USA, 2005.
  152. Daniluk, P., Szajkowski, L., Kryshtafovych, A., and Fidelis, K. (2004). Identifying model-target similarity using local descriptors of protein structure. Sixth Meeting on the Critical Assessment of Protein Structure Prediction, Gaeta, Italy, December, 2004, p.162.
  153. Daniluk, P., Kryshtafovych, A., Hvidsten, T. R., Komorowski, J. & Fidelis, K. (2004). Identifying Structural Similarity of Proteins Using Local Descriptors of Protein Structure. Pac. Symp. Biocomput., HI, USA, January, 2004, p.61.
  154. Wilczynski, B., Hvidsten, T. R., Kryshtafovych, A., Komorowski, J. & Fidelis, K. (2004). An iterative approach to gene regulation pathways discovery. Pac. Symp. Biocomput., HI, USA, January, 2004, p.140.
  155. Kryshtafovych, A., Hvidsten, T.R., Komorowski, J., Daniluk, P., Wilczynska, M. and Fidelis, K. (2003). Automated local structure based classification of protein folds. Pacific Symposium on Biocomputing, HI, USA, January 2-7, 2003, p. 98.
  156. Hvidsten, T.R., Kryshtafovych, A., Komorowski, J. and Fidelis, K. (2003). Identifying gene regulation mechanisms using rule based classifiers. Pacific Symposium on Biocomputing. HI, USA, January 2-7, 2003, p. 87.
  157. Hvidsten, T.R., Wilczynski, B., Kryshtafovych, A., Stubbs, L., Komorowski, J. and Fidelis, K. (2003). Identifying gene regulation mechanisms using rule based classifiers. Systems biology: Genomic approaches to transcriptional regulation. Cold Spring Harbor, NY, USA, 2003, p. 34.
  158. Nowakowski, S., Kryshtafovych, A., Fidelis, K. & Tiuryn, J. (2003). Detecting local structure motifs in proteins by analyzing motif sequence signatures. European Conference on Computational Biology, Paris, France, 2003.
  159. Hvidsten, T.R., Kryshtafovych, A., Komorowski, J. and Fidelis, K. (2003). Applying sequence derived features from similar 3-d local structures to protein fold recognition. RECOMB. Berlin, Germany, April, 2003, p. 191.
  160. Wilczynski, B., Hvidsten, T.R., Kryshtafovych, A., Stubbs, L., Komorowski, J. and Fidelis, K. (2003). Identifying gene regulation mechanisms based on local gene expression similarities using rule based classifiers. RECOMB. Berlin, Germany, April, 2003, p. 293.
  161. Hvidsten, T.R., Kryshtafovych, A., Zemla, A., Vemuri, R., Komorowski, J. and Fidelis, K. (2002). Applying rule based classifiers to protein fold recognition. Abstracts of Pacific Symposium on Biocomputing PSB 2002. Hawaii (USA), January 3-7, 2002, 83.
  162. Martynyak, R.M., Kryshtafovych, A.A. and Nagalka, S.P. (2000) Simulation of thermomechanical behavior of bimaterial containing an interface crack with rough faces. Abstracts of 13rd European Conference on Fracture. San Sebastian (Spain), September 6-9, 2000, 251.
  163. Kit, H., Martynyak, R. and Kryshtafovych, A. (1999). Thermomechanics of contact phenomena in bodies with interface flaws. Abstracts of 4th International Symposium of Ukrainian Mechanical Engineers in Lviv. May 19-21, 1999, 9.
  164. Shvets, R., Martynyak, R., Kryshtafovych, A., and Machyshyn, I. (1999). Imperfect contact of bodies due to an action of concentrated thermal and force factors. Abstracts of the 3rd Ukrainian-Polish scientific Symposium "Mixed Problems in Mechanics of Inhomogeneous Structures". Lviv (Ukraine), September 7-11, 1999, 26.
  165. Kryshtafovych, A.A., Martynyak, R.M. and Shvets R.M. (1998). Influence of surface irregularities on interaction of heat conducting anisotropic bodies. Proc. of the International Conference «Modern Problems of Mechanics and Mathematics», dedicated to the 70th anniversary of Academician Ya.S. Pidstryhach. Lviv, May 25-28, 1998, 174.*
  166. Shvets, R.M., Kryshtafovych, A.A. and Martynyak, R.M. (1998). Effect of thin interface layers on thermoelastic instability of solid contact. Abstracts of 13th US National Congress of Applied Mechanics. Gainesville, FL (USA), June 21-26, 1998, WB5.
  167. Martynyak, R.M. and Kryshtafovych, A.A. (1997). Propagation of prefailure zones in bimaterial near interface crack with contacting thermoresistant faces. Abstracts of International Conference and Exhibition on Micro Materials «MicroMat '97». Berlin (Germany), April 16-18, 1997, 507.
  168. Kryshtafovych, A.A. and Martynyak, R.M. (1997). Influence of materials anisotropy on perfectness of thermomechanical contact of bodies with thermophysical surface irregularities. Abstracts of International Conference and Exhibition on Micro Materials «MicroMat '97». Berlin (Germany), April 16-18, 1997, 508.
  169. Shvets, R.M. and Kryshtafovych, A.A. (1997). Thermomechanical contact of anisotropic half-planes in a presence of local zones of thermal resistance at the interface. Abstracts of the 3rd EUROMECH Solid Mechanics Conference. Stockholm (Sweden), August 18-22, 1997, 73.
  170. Kryshtafovych, A.A. and Shvets, R.M. (1996). On strength of the system of mated anisotropic bodies with a surface recess. Proceedings of the 2nd International Symposium «Mechanics & Physics of Building Materials & Constructions». Lviv/Dubliany (Ukraine), October 7-10, 1996, 62.*
  171. Kryshtafovych, A.A. (1995). Redistribution of contact pressure near the thermoinsulated zones at the interface of two anisotropic half-spaces. Publ. #4-95 of Institute for Applied Problems in Mechanics and Mathematics, National Academy of Sciences of Ukraine 1995, 12.
  172. Shvets, R.M. and Kryshtafovych, A.A. (1995). Investigation of thermoelastic behavior of mated anisotropic half-spaces with uneven contact surfaces. Abstracts of the 4th International Conference «Mechanics of Inhomogeneous Structures». Ternopil' (Ukraine), September 19-21, 1995, 198.
  173. Kryshtafovych, A.A. (1995). Two-dimensional problems on interaction of anisotropic bodies at imperfect heat and mechanical contact. Resume of the Ph.D. theses.- Institute for Applied Problems in Mechanics and Mathematics, National Academy of Sciences of Ukraine - L'viv, 1995.
  174. Kryshtafovych, A.A. (1994). On symmetry of the gap shape at the compression of the anisotropic half-plane with a rigid one. Publ. #6-94 of Institute for Applied Problems in Mechanics and Mathematics, National Academy of Sciences of Ukraine 1994, 23.
  175. Kryshtafovych, A.A. (1993). Some aspects of contact interaction of anisotropic bodies with geometric surface irregularities. Proceedings of the 18th Conference of Young Scientists at the Institute of Mechanics, Academy of Sciences of Ukraine. Kyiv, May 18-21, 1993, p.58.*
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* Conference Papers