Publications related to
local descriptors of protein structure

Articles using local descriptors

• T. R. Hvidsten, A. Lægreid, A. Kryshtafovych, G. Andersson, K. Fidelis and J. Komorowski. A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PLoS ONE 4(7): e6266, 2009.
• P. Björkholm, P. Daniluk, A. Krystofovich, K. Fidelis, R. Andersson and TR Hvidsten. Using multi-data hidden Markov models trained on local neigh-borhoods of protein structure to predict residue-residue contacts. Bioinformatics 25: 1264-1270, 2009.
  
• T. R. Hvidsten*, A. Kryshtafovych* and K. Fidelis. Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions, Proteins: Structure, Function, and Bioinformatics 75 (4): 870-884, 2009.
  
• H. Strömbergsson, P. Daniluk, A. Kryshtafovych, K. Fidelis, J. E. S. Wikberg, G. J. Kleywegt and T. R. Hvidsten. Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space, Journal of Chemical Information and Modeling 48 (11): 2278–2288, 2008.
  
• A. Kryshtafovych, A. Prlic, Z. Dmytriv, P. Daniluk, M. Milostan, V. Eyrich, T. Hubbard, K. Fidelis. New tools and expanded data analysis capabilities at the protein structure prediction center. Proteins: Structure, Function and Bioinformatics 69 (S8): 19-26, 2007.
• M. Drabikowski, S. Nowakowski and J. Tiuryn. Library of local descriptors models the core of proteins accurately. Proteins: Structure, Function and Bioinformatics 69: 499-510, 2007.
  
• S. Nowakowski and M. Drabikowski. Efficient Local Protein Structure Prediction, Lecture Notes in Computer Science 4481: 308-315, Springer-Verlag Berlin Heidelberg New York, 2007.
• H. Strömbergsson, A. Kryshtafovych, P. Prusis, K. Fidelis, J. E. S. Wikberg, J. Komorowski and T. R. Hvidsten. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures, Proteins: Structure, Function and Bioinformatics 65: 568-579, 2006.
• S. Nowakowski, K. Fidelis and J. Tiuryn. Introducing Dependencies into Alignment Analysis and Its Use for Local Structure Prediction in Proteins, Lecture Notes in Computer Science 3911: 1106-1113, Springer-Verlag Berlin Heidelberg New York, 2006.
• A. Kryshtafovych, M. Milostan, L. Szajkowski, P. Daniluk and K. Fidelis. CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins: Structure, Function and Bioinformatics 61 (S7): 19-23, 2005.
  
• T. R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins, ECCB2003, Bioinformatics 19 Suppl 2: II81-II91, 2003.
  

*Contributed equally.

Reviews mentioning local descriptors

• T. R. Hvidsten and J. Komorowski. Rough sets in bioinformatics, Transactions on Rough Sets VII edited by E. Orlowska, J. F. Peters and A. Skowron, Lecture notes in computer science 4400: 225-243, Springer-Verlag Berlin Heidelberg New York, 2007.
• J. M. Bujnicki. Protein-Structure Prediction by Recombination of Fragments. ChemBioChem 7: 19 - 27, 2005.

Thesis using local descriptors

• Helena Strömmbergsson. Chemogenomics: Models of Protein-Ligand Interaction Space, PhD Thesis, Uppsala University, 2009.
• Patrik Björkholm. Method for recognizing local descriptors of protein structures using Hidden Markov Models, Master thesis, 2008.
• Johan Alexander Källberg Zvrskovec. Protein structure prediction by search among combinations of reoccurring structural components, Student project (10 points), Uppsala University, 2008.
• M. Drabikowski. Groups and signals analyzes. Assembling proteins structure from local descriptors. PhD Thesis, University of Warsaw, 2006.
• S. Nowakowski. Estimating Probability Distributions of a Sequence Occuring in an Alignment and Its Use in 3D Protein Structure Prediction. PhD thesis, Insitute of Informatics, Warsaw University, 2006.
• Minyan Hong. Fold recognition using local descriptors of protein structure and Hidden Markov Models , Student project (10 points), 2006 and Master thesis, Uppsala University, 2007.
• Marta Luksza. A System for Predicting Protein Function from Structure, Master thesis, Uppsala University, 2005.
• Anna Hennecke. Predicting protein function from its 3-dimensional structure - Biological validation of protein function predictions, Student project (10 points), Uppsala University, 2005.
• T. R. Hvidsten. Predicting function of genes and proteins from sequence, structure and expression data, PhD thesis, Department of Information Technology and Linnaeus Centre for Bioinformatics, Uppsala University, 2004.