Project Scientist
Genome Center, University of California, Davis,
451 Health Sciences Dr., Davis CA 95616-8816, USA

E-mail:
Tel./Fax. : +1 (530) 754-8977

Research Interests

• protein structure prediction, analysis and classification
• evaluation of protein models
• assessment of methods for template-based modeling, free modeling, refinement, data-assisted modeling, quaternary structure modeling
• validation of cryo-EM models
• assessment of model accuracy assessment methods
• prediction and assessment of inter-residue contacts
• assessment of disorder prediction methods
• identification of gene regulation mechanisms
• detection of protein function from sequence
• prediction of enzyme-ligand interactions

Selected Publications (All Publications)

• Petascale Homology Search for Structure Prediction.
  Cold Spring Harb Perspect Biol. 2024; a041465.
  Lee S, Kim G, Karin L, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M.

• Critical assessment of methods of protein structure prediction (CASP) - round XV.
  Proteins. 2023; 91(12):1539-1549.
  Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J.

• The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15.
  Proteins. 2023; 91(12):1636-1657
  Ozden B, Kryshtafovych A, Karaca E.

• Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.
  Proteins. 2023; 91(12):1903-1911
  Kryshtafovych A, Montelione GT, Rigden DJ, Mesdaghi S, Karaca E, Moult J.

• Critical assessment of methods of protein structure prediction (CASP) - round XIV.
  Proteins. 2021; 89(12):1607-1617
  Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J.

• Computational models in the service of X-ray and cryo-electron microscopy structure determination.
  Proteins. 2021; 89(12):1633-1646
  Kryshtafovych A, Moult J, ..., AlphaFold2 team.

• Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14).
  Proteins. 2021; 89(12):1673-1686
  Kinch L, Pei J, Kryshtafovych A, ..., Grishin N.

• Modeling SARS-CoV-2 proteins in the CASP-commons experiment.
  Proteins. 2021; 89(12):1987-1996
  Kryshtafovych A, Moult J, ..., CASP-COVID participants.

• Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
  Nature Methods. 2021; 18:156-164. https://doi.org/10.1038/s41592-020-01051-w
  Lawson CL, Kryshtafovych A, ..., Chiu W.

• Cryo-electron microscopy targets in CASP13: overview and evaluation results.
  Proteins. 2019; 87(12):1128-1140
  Kryshtafovych A, Malhotra S, ..., Topf M.

• Evaluation system and web infrastructure for the second cryo-EM model challenge.
  J Struct Biol. 2018; 204(1):96-108
  Kryshtafovych A, Adams PD, Lawson CL, Chiu W.

• Assessment of model accuracy estimations in CASP12.
  Proteins. 2018; 86(S1):345-360
  Kryshtafovych A, Monastyrskyy B, ..., Tramontano A

• Evaluation of the template-based modeling in CASP12.
  Proteins. 2018; 86(S1):321-334.
  Kryshtafovych A, Monastyrskyy B, ..., Tramontano A.

• New encouraging developments in contact prediction: Assessment of the CASP11 results.
  Proteins. 2015; Published online: doi: 10.1002/prot.24943. PMID: 26474083
  Monastyrskyy B, D'Andrea D, ..., Kryshtafovych A

• Evaluation of disorder predictions in CASP9
  Proteins. 2011; 79(S10):107-118
  Monastyrskyy B, Fidelis K, ..., Kryshtafovych A

• Protein structure prediction and model quality assessment
  Drug Discov Today. 2009 Apr; 14(7-8):386-393.
  Kryshtafovych A, Fidelis K.

• Discovering regulatory binding-site modules using rule-based learning
  Genome Res. 2005 Jun;15(6):856-66. PMID: 15930496
  Hvidsten TR, Wilczynski B, Kryshtafovych A, ..., Fidelis K

• A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins
  Bioinformatics. 2003 Oct;19 Suppl 2:ii81-91.
  Hvidsten TR, Kryshtafovych A, Komorowski J, Fidelis K