All Stories

  1. Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score

    Article • Acta Crystallographica Section D Structural Biology, January 2023, International Union of Crystallography

    Daisuke Kihara

  2. Survey of Machine Learning Techniques for Prediction of the Isoform Specificity of Cytochrome P450 Substrates

    Article • Current Drug Metabolism, May 2019, Bentham Science Publishers

    Daisuke Kihara, Dr. Dongqing Huang Wei

  3. A global map of the protein shape universe

    Article • PLoS Computational Biology, April 2019, PLOS

    Daisuke Kihara

  4. De novo main-chain modeling for EM maps using MAINMAST

    Article • Nature Communications, April 2018, Springer Science + Business Media

    Daisuke Kihara

  5. Modeling the assembly order of multimeric heteroprotein complexes

    Article • PLoS Computational Biology, January 2018, PLOS

    Daisuke Kihara

  6. Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER

    Article • December 2017, Wiley

    Daisuke Kihara

  7. In silico structure-based approaches to discover protein-protein interaction-targeting drugs

    Article • Methods, December 2017, Elsevier

    Daisuke Kihara

  8. Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions

    Article • Proteins Structure Function and Bioinformatics, September 2017, Wiley

    Daisuke Kihara

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

    Article • Proteins Structure Function and Bioinformatics, September 2017, Wiley

    Daisuke Kihara

  10. DextMP: deep dive into text for predicting moonlighting proteins

    Article • Bioinformatics, July 2017, Oxford University Press (OUP)

    Daisuke Kihara

  11. Variability of Protein Structure Models from Electron Microscopy

    Article • Structure, April 2017, Elsevier

    Daisuke Kihara

  12. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology

    Article • BMC Bioinformatics, March 2017, Springer Science + Business Media

    Daisuke Kihara

  13. Using PFP and ESG Protein Function Prediction Web Servers

    Article • January 2017, Springer Science + Business Media

    Daisuke Kihara

  14. Predicting Real-Valued Protein Residue Fluctuation Using FlexPred

    Article • October 2016, Springer Science + Business Media

    Daisuke Kihara

  15. Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions

    Article • Proteins Structure Function and Bioinformatics, October 2016, Wiley

    Daisuke Kihara

  16. Missing gene identification using functional coherence scores

    Article • Scientific Reports, August 2016, Springer Science + Business Media

    Daisuke Kihara

  17. PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation

    Article • Journal of Chemical Information and Modeling, August 2016, American Chemical Society (ACS)

    Daisuke Kihara

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

    Article • Proteins Structure Function and Bioinformatics, June 2016, Wiley

    Daisuke Kihara, Dr. Alexandre M.J.J. Bonvin

  19. Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations

    Article • Journal of Computational Chemistry, May 2016, Wiley

    Daisuke Kihara

  20. Genome-scale prediction of moonlighting proteins using diverse protein association information

    Article • Bioinformatics, March 2016, Oxford University Press (OUP)

    Daisuke Kihara

  21. Pl-Patchsurfer: A Fast, Surface-Patch-Based Virtual Screening Program using Three-Dimensional Zernike Descriptors

    Article • Biophysical Journal, February 2016, Elsevier

    Daisuke Kihara

  22. Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein–Ligand Binding Prediction in CSAR 2013 and 2014

    Article • Journal of Chemical Information and Modeling, December 2015, American Chemical Society (ACS)

    Daisuke Kihara

  23. Protein structure prediction using residue- and fragment-environment potentials in CASP11

    Article • Proteins Structure Function and Bioinformatics, September 2015, Wiley

    Daisuke Kihara

  24. Computational characterization of moonlighting proteins: Table 1

    Article • Biochemical Society Transactions, December 2014, Portland Press Ltd.

    Daisuke Kihara

  25. Detecting local residue environment similarity for recognizing near-native structure models

    Article • Proteins Structure Function and Bioinformatics, October 2014, Wiley

    Daisuke Kihara

  26. Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

    Article • Bioinformatics, October 2014, Oxford University Press (OUP)

    Daisuke Kihara

  27. Assessment of protein side-chain conformation prediction methods in different residue environments

    Article • Proteins Structure Function and Bioinformatics, March 2014, Wiley

    Daisuke Kihara

  28. 3D-SURFER 2.0: Web Platform for Real-Time Search and Characterization of Protein Surfaces

    Article • January 2014, Springer Science + Business Media

    Daisuke Kihara

  29. Protein domain recurrence and order can enhance prediction of protein functions

    Article • Bioinformatics, September 2012, Oxford University Press (OUP)

    Daisuke Kihara

  30. Multi-LZerD: Multiple protein docking for asymmetric complexes

    Article • Proteins Structure Function and Bioinformatics, January 2012, Wiley

    Daisuke Kihara

  31. Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking

    Article • Current Protein and Peptide Science, September 2011, Bentham Science Publishers

    Daisuke Kihara

  32. Quality Assessment of Protein Structure Models

    Article • Current Protein and Peptide Science, June 2009, Bentham Science Publishers

    Daisuke Kihara

  33. ESG: extended similarity group method for automated protein function prediction

    Article • Bioinformatics, May 2009, Oxford University Press (OUP)

    Daisuke Kihara

  34. Protein-protein docking using region-based 3D Zernike descriptors

    Article • BMC Bioinformatics, January 2009, Springer Science + Business Media

    Daisuke Kihara

  35. New paradigm in protein function prediction for large scale omics analysis

    Article • Molecular BioSystems, January 2008, Royal Society of Chemistry

    Daisuke Kihara

  36. FUNCTION PREDICTION OF UNCHARACTERIZED PROTEINS

    Article • Journal of Bioinformatics and Computational Biology, February 2007, World Scientific Pub Co Pte Lt

    Daisuke Kihara

  37. Enhanced automated function prediction using distantly related sequences and contextual association by PFP

    Article • Protein Science, June 2006, Wiley

    Daisuke Kihara

  38. The PDB is a Covering Set of Small Protein Structures

    Article • Journal of Molecular Biology, December 2003, Elsevier

    Daisuke Kihara

  39. TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints

    Article • Proceedings of the National Academy of Sciences, August 2001, Proceedings of the National Academy of Sciences

    Daisuke Kihara