| 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 (S1), 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 | 158 | 2011 |
| Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013 | 115 | 2013 |
| Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking D Kihara, L Sael, R Chikhi, J Esquivel-Rodriguez Current Protein and Peptide Science 12 (6), 520-530, 2011 | 111 | 2011 |
| Multi‐LZerD: Multiple protein docking for asymmetric complexes J Esquivel‐Rodríguez, YD Yang, D Kihara Proteins: Structure, Function, and Bioinformatics 80 (7), 1818-1833, 2012 | 102 | 2012 |
| 3D-SURFER: software for high-throughput protein surface comparison and analysis D La, J Esquivel-Rodríguez, V Venkatraman, B Li, L Sael, S Ueng, ... Bioinformatics 25 (21), 2843-2844, 2009 | 92 | 2009 |
| Tuning of Pectin Methylesterification PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER F Sénéchal, M L'Enfant, JM Domon, E Rosiau, MJ Crépeau, O Surcouf, ... Journal of Biological Chemistry 290 (38), 23320-23335, 2015 | 68 | 2015 |
| Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite J Esquivel-Rodriguez, V Filos-Gonzalez, B Li, D Kihara Protein Structure Prediction, 209-234, 2014 | 53 | 2014 |
| Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors J Esquivel-Rodríguez, D Kihara The Journal of Physical Chemistry B 116 (23), 6854-6861, 2012 | 49 | 2012 |
| Computational methods for constructing protein structure models from 3D electron microscopy maps J Esquivel-Rodríguez, D Kihara Journal of structural biology 184 (1), 93-102, 2013 | 47 | 2013 |
| Modeling the assembly order of multimeric heteroprotein complexes LX Peterson, Y Togawa, J Esquivel-Rodriguez, G Terashi, C Christoffer, ... PLoS computational biology 14 (1), e1005937, 2018 | 36 | 2018 |
| Ranking protein–protein docking results using steered molecular dynamics and potential of mean force calculations LJ Kingsley, J Esquivel‐Rodríguez, Y Yang, D Kihara, MA Lill Journal of computational chemistry 37 (20), 1861-1865, 2016 | 32 | 2016 |
| Navigating 3D electron microscopy maps with EM-SURFER J Esquivel-Rodríguez, Y Xiong, X Han, S Guang, C Christoffer, D Kihara BMC bioinformatics 16, 1-9, 2015 | 26 | 2015 |
| Human and server docking prediction for CAPRI round 30‐35 using LZerD with combined scoring functions LX Peterson, H Kim, J Esquivel‐Rodriguez, A Roy, X Han, WH Shin, ... Proteins: Structure, Function, and Bioinformatics 85 (3), 513-527, 2017 | 19 | 2017 |
| 3D-SURFER 2.0: Web Platform for Real-Time Search and Characterization of Protein Surfaces Y Xiong, J Esquivel-Rodriguez, L Sael, D Kihara Protein Structure Prediction, 105-117, 2014 | 13 | 2014 |
| Evaluation of multiple protein docking structures using correctly predicted pairwise subunits J Esquivel-Rodríguez, D Kihara BMC bioinformatics 13, 1-4, 2012 | 11 | 2012 |
| Effect of conformation sampling strategies in genetic algorithm for multiple protein docking J Esquivel-Rodríguez, D Kihara BMC proceedings 6, 1-6, 2012 | 9 | 2012 |
| MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field E Alnabati, J Esquivel-Rodriguez, G Terashi, D Kihara Frontiers in Molecular Biosciences 9, 935411, 2022 | 7 | 2022 |
| EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization M Zumbado-Corrales, J Esquivel-Rodríguez Biomimetics 6 (2), 37, 2021 | 5 | 2021 |
| Graphical Models for Protein Function and Structure Prediction M Tang, KM Tan, X Tan, L Sael, M Chitale, J Esquivel‐Rodríguez, ... Biological Knowledge Discovery Handbook: Preprocessing, Mining, and …, 2014 | 5 | 2014 |
Daisuke KiharaProfessor of Biological Sciences and Computer Science, Showalter University Faculty Scholar, PurdueVerified email at purdue.edu