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

Current Research Interests

• protein structure prediction, analysis and classification
• evaluation of protein models
• identification of gene regulation mechanisms
• detection of protein function from sequence
• prediction of enzyme-ligand interactions
• prediction and assessment of inter-residue contacts in proteins
• assessment of disorder in proteins
• assessment of protein model quality
  

Selected Publications

• Critical assessment of methods of protein structure prediction (CASP) - round IX
  Proteins. 2011; 79(S10):1-5
  Moult J, Fidelis K, Kryshtafovych A, Tramontano A

• Evaluation of model quality predictions in CASP9
  Proteins. 2011; 79(S10):91-106
  Kryshtafovych A, Fidelis K, Tramontano A

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

• Evaluation of residue-residue contact predictions in CASP9
  Proteins. 2011; 79(S10):119-125
  Monastyrskyy B, Fidelis K, Tramontano A, Kryshtafovych A

• CASP9 results compared to those of previous CASP experiments
  Proteins. 2011; 79(S10):196-207
  Kryshtafovych A, Fidelis K, Moult J

• Evaluation of template-based models in CASP8 with standard measures
  Proteins. 2009 Aug 5; 77(S9):18-28
  Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A

• A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity
  PLoS One. 2009 Jul; 4(7):e6266.
  Hvidsten TR, Legreid A, Kryshtafovych A, Andersson G, Fidelis K, Komorowski J

• Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts
  Bioinformatics. 2009 Mar; 25:1264-1270.
  Bjorkholm P, Daniluk P, Kryshtafovych A, Fidelis K, Andersson R, Hvidsten TR

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

• Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions.
  Proteins. 2009 Jun; 75(4):870-884. (Avail. online 2008, Oct 15).
  Hvidsten TR, Kryshtafovych A, Fidelis K.

• Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space
  J Chem Inf Model. 2008 Oct 21; 48(11):2278-2288. PMID: 18937438
  Strombergsson H, Daniluk P, Kryshtafovych A, Fidelis K, Wikberg JE, Kleywegt GJ, Hvidsten TR.

• 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, Tiuryn J, Komorowski J, 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