| The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling J Li, R Abel, K Zhu, Y Cao, S Zhao, RA Friesner Proteins: Structure, Function, and Bioinformatics 79 (10), 2794-2812, 2011 | 893 | 2011 |
| Docking covalent inhibitors: a parameter free approach to pose prediction and scoring K Zhu, KW Borrelli, JR Greenwood, T Day, R Abel, RS Farid, E Harder Journal of chemical information and modeling 54 (7), 1932-1940, 2014 | 383 | 2014 |
| Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction K Zhu, T Day, D Warshaviak, C Murrett, R Friesner, D Pearlman Proteins: Structure, Function, and Bioinformatics 82 (8), 1646-1655, 2014 | 206 | 2014 |
| Structure-based virtual screening approach for discovery of covalently bound ligands D Toledo Warshaviak, G Golan, KW Borrelli, K Zhu, O Kalid Journal of chemical information and modeling 54 (7), 1941-1950, 2014 | 145 | 2014 |
| Long loop prediction using the protein local optimization program K Zhu, DL Pincus, S Zhao, RA Friesner Proteins: Structure, Function, and Bioinformatics 65 (2), 438-452, 2006 | 143 | 2006 |
| Improved methods for side chain and loop predictions via the protein local optimization program: variable dielectric model for implicitly improving the treatment of … K Zhu, MR Shirts, RA Friesner Journal of Chemical Theory and Computation 3 (6), 2108-2119, 2007 | 123 | 2007 |
| Toward better refinement of comparative models: predicting loops in inexact environments BD Sellers, K Zhu, S Zhao, RA Friesner, MP Jacobson Proteins: Structure, Function, and Bioinformatics 72 (3), 959-971, 2008 | 101 | 2008 |
| Successful prediction of the intra-and extracellular loops of four G-protein-coupled receptors DA Goldfeld, K Zhu, T Beuming, RA Friesner Proceedings of the National Academy of Sciences 108 (20), 8275-8280, 2011 | 85 | 2011 |
| Selection of Nanobodies that Block the Enzymatic and Cytotoxic Activities of the Binary Clostridium Difficile Toxin CDT M Unger, AM Eichhoff, L Schumacher, M Strysio, S Menzel, C Schwan, ... Scientific reports 5 (1), 7850, 2015 | 72 | 2015 |
| Progress in super long loop prediction S Zhao, K Zhu, J Li, RA Friesner Proteins: Structure, Function, and Bioinformatics 79 (10), 2920-2935, 2011 | 51 | 2011 |
| Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling X Li, MP Jacobson, K Zhu, S Zhao, RA Friesner Proteins: Structure, Function, and Bioinformatics 66 (4), 824-837, 2007 | 48 | 2007 |
| Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein− Ligand Complexes K Zhu, MR Shirts, RA Friesner, MP Jacobson Journal of Chemical Theory and Computation 3 (2), 640-648, 2007 | 45 | 2007 |
| Ab initio structure prediction of the antibody hypervariable H3 loop K Zhu, T Day Proteins: Structure, Function, and Bioinformatics, 2012 | 37 | 2012 |
| Cloning and characterization of rat spermatid protein SSP411: a thioredoxin‐like protein HJ Shi, AZ Wu, M Santos, ZM Feng, L Huang, YM Chen, K Zhu, ... Journal of andrology 25 (4), 479-493, 2004 | 27 | 2004 |
| Loop prediction for a GPCR homology model: algorithms and results DA Goldfeld, K Zhu, T Beuming, RA Friesner Proteins: Structure, Function, and Bioinformatics 81 (2), 214-228, 2013 | 26 | 2013 |
| Prediction of long loops with embedded secondary structure using the protein local optimization program EB Miller, CS Murrett, K Zhu, S Zhao, DA Goldfeld, JH Bylund, ... Journal of chemical theory and computation 9 (3), 1846-1864, 2013 | 16 | 2013 |
| Induced-fit docking enables accurate free energy perturbation calculations in homology models T Xu, K Zhu, A Beautrait, J Vendome, KW Borrelli, R Abel, RA Friesner, ... Journal of Chemical Theory and Computation 18 (9), 5710-5724, 2022 | 11 | 2022 |
| Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors K Zhu, C Li, KY Wu, C Mohr, X Li, B Lanman Journal of Computer-Aided Molecular Design 36 (8), 591-604, 2022 | 6 | 2022 |
| Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein–coupled receptors DA Goldfeld, K Zhu, T Beuming, RA Friesner Proceedings of the National Academy of Sciences 108 (30), E342-E342, 2011 | 3 | 2011 |
| Heterocyclic spiro compounds and methods of use BA Lanman, A Banerjee, CHUM Margaret, D Dai, J Eshon, D Huang, ... US Patent App. 18/032,548, 2024 | | 2024 |
Matthew JacobsonUCSFVerified email at ucsf.edu
Matthew JacobsonUCSFVerified email at ucsf.edu