A large-scale evaluation of computational protein function prediction P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ... Nature methods 10 (3), 221-227, 2013 | 1062 | 2013 |
An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ... Genome biology 17, 1-19, 2016 | 416 | 2016 |
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019 | 368 | 2019 |
Limitations and potentials of current motif discovery algorithms J Hu, B Li, D Kihara Nucleic acids research 33 (15), 4899-4913, 2005 | 312 | 2005 |
Protein-protein docking using region-based 3D Zernike descriptors V Venkatraman, YD Yang, L Sael, D Kihara BMC bioinformatics 10, 1-21, 2009 | 215 | 2009 |
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm J Skolnick, D Kihara, Y Zhang Proteins: Structure, Function, and Bioinformatics 56 (3), 502-518, 2004 | 214 | 2004 |
TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints D Kihara, H Lu, A Kolinski, J Skolnick Proceedings of the National Academy of Sciences 98 (18), 10125-10130, 2001 | 184 | 2001 |
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding Y Zhang, D Kihara, J Skolnick Proteins: Structure, Function, and Bioinformatics 48 (2), 192-201, 2002 | 181 | 2002 |
Enhanced automated function prediction using distantly related sequences and contextual association by PFP T Hawkins, S Luban, D Kihara Protein Science 15 (6), 1550-1556, 2006 | 175 | 2006 |
Structure and inhibition of EV-D68, a virus that causes respiratory illness in children Y Liu, J Sheng, A Fokine, G Meng, WH Shin, F Long, RJ Kuhn, D Kihara, ... Science 347 (6217), 71-74, 2015 | 171 | 2015 |
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 168 | 2016 |
Community-wide assessment of protein-interface modeling suggests improvements to design methodology SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Journal of molecular biology 414 (2), 289-302, 2011 | 157 | 2011 |
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data T Hawkins, M Chitale, S Luban, D Kihara Proteins: Structure, Function, and Bioinformatics 74 (3), 566-582, 2009 | 157 | 2009 |
Defrosting the frozen approximation: PROSPECTOR—a new approach to threading J Skolnick, D Kihara Proteins: Structure, Function, and Bioinformatics 42 (3), 319-331, 2001 | 152 | 2001 |
Fast protein tertiary structure retrieval based on global surface shape similarity L Sael, B Li, D La, Y Fang, K Ramani, R Rustamov, D Kihara Proteins: Structure, Function, and Bioinformatics 72 (4), 1259-1273, 2008 | 150 | 2008 |
The PDB is a covering set of small protein structures D Kihara, J Skolnick Journal of molecular biology 334 (4), 793-802, 2003 | 146 | 2003 |
Function prediction of uncharacterized proteins T Hawkins, D Kihara Journal of bioinformatics and computational biology 5 (01), 1-30, 2007 | 133 | 2007 |
The effect of long‐range interactions on the secondary structure formation of proteins D Kihara Protein Science 14 (8), 1955-1963, 2005 | 121 | 2005 |
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ... Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 | 119 | 2019 |
Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors V Venkatraman, L Sael, D Kihara Cell biochemistry and biophysics 54, 23-32, 2009 | 114 | 2009 |