| ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers BG Pierce, K Wiehe, H Hwang, BH Kim, T Vreven, Z Weng Bioinformatics 30 (12), 1771-1773, 2014 | 1587 | 2014 |
| Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors J Wang, J Zhuang, S Iyer, XY Lin, TW Whitfield, MC Greven, BG Pierce, ... Genome research 22 (9), 1798-1812, 2012 | 1063 | 2012 |
| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 618 | 2020 |
| Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library BG Pierce, Y Hourai, Z Weng PloS one 6 (9), e24657, 2011 | 618 | 2011 |
| ZRANK: reranking protein docking predictions with an optimized energy function B Pierce, Z Weng PROTEINS: Structure, Function, and Bioinformatics 67 (4), 1078-1086, 2007 | 512 | 2007 |
| Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2 T Vreven, IH Moal, A Vangone, BG Pierce, PL Kastritis, M Torchala, ... Journal of molecular biology 427 (19), 3031-3041, 2015 | 440 | 2015 |
| Factorbook. org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium J Wang, J Zhuang, S Iyer, XY Lin, MC Greven, BH Kim, J Moore, ... Nucleic acids research 41 (D1), D171-D176, 2012 | 437 | 2012 |
| Integrating statistical pair potentials into protein complex prediction J Mintseris, B Pierce, K Wiehe, R Anderson, R Chen, Z Weng Proteins: Structure, Function, and Bioinformatics 69 (3), 511-520, 2007 | 380 | 2007 |
| Protein–protein docking benchmark 2.0: an update J Mintseris, K Wiehe, B Pierce, R Anderson, R Chen, J Janin, Z Weng Proteins: Structure, Function, and Bioinformatics 60 (2), 214-216, 2005 | 370 | 2005 |
| Protein–protein docking benchmark version 3.0 H Hwang, B Pierce, J Mintseris, J Janin, Z Weng Proteins: Structure, Function, and Bioinformatics 73 (3), 705-709, 2008 | 311 | 2008 |
| M-ZDOCK: a grid-based approach for Cn symmetric multimer docking B Pierce, W Tong, Z Weng Bioinformatics 21 (8), 1472-1478, 2005 | 217 | 2005 |
| Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants R Yin, BY Feng, A Varshney, BG Pierce Protein Science 31 (8), e4379, 2022 | 193 | 2022 |
| A combination of rescoring and refinement significantly improves protein docking performance B Pierce, Z Weng Proteins: Structure, Function, and Bioinformatics 72 (1), 270-279, 2008 | 174 | 2008 |
| 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 |
| ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5 K Wiehe, B Pierce, J Mintseris, WW Tong, R Anderson, R Chen, Z Weng Proteins: Structure, Function, and Bioinformatics 60 (2), 207-213, 2005 | 127 | 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 | 120 | 2019 |
| 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 | 114 | 2013 |
| Structure‐based design of a T‐cell receptor leads to nearly 100‐fold improvement in binding affinity for pepMHC JN Haidar, B Pierce, Y Yu, W Tong, M Li, Z Weng Proteins: Structure, Function, and Bioinformatics 74 (4), 948-960, 2009 | 103 | 2009 |
| Computational design of the affinity and specificity of a therapeutic T cell receptor BG Pierce, LM Hellman, M Hossain, NK Singh, CW Vander Kooi, Z Weng, ... PLoS computational biology 10 (2), e1003478, 2014 | 96 | 2014 |
Zhiping WengProf & Chair, Department of Genomics and Computational Biology, UMASS Medical SchoolVerified email at umassmed.edu
