Cited by 1,393Protein Structure and DynamicsComputational Drug Discovery MethodsEnzyme Structure and Function

The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.

ZDOCK: An initial‐stage protein‐docking algorithm

Chen, Rong, Li, Li, Weng, Zhiping·2003·Proteins: Structure, Function, and Bioinformatics

Open this paper in CoChat — free account

Abstract

The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody‐antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near‐native structure within the top 2000 predictions at the 6° rotational sampling density, with an average of 52 near‐native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/∼rong/dock. Proteins 2003;52:80–87. © 2003 Wiley‐Liss, Inc.

Integrity signals

Registry

Crossref · 10.1002/prot.10389

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
The interpretation of protein structures: Estimation of static accessibility
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
Gabb, H. A., Jackson, R. M., & Sternberg, M. J. E. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1203 · Cited by 820
Determination of atomic desolvation energies from the structures of crystallized proteins
Zhang, C., Vasmatzis, G., Cornette, J. L., & DeLisi, C. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0859 · Cited by 537
Flexible protein–ligand docking by global energy optimization in internal coordinates
Totrov, M. M., & Abagyan, R. A. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(1997)1+ · Cited by 451
Prediction of protein–protein interactions by docking methods
Smith, G. R., & Sternberg, M. J. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00285-3 · Cited by 450
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
Chen, R., & Weng, Z. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10092 · Cited by 375
Self-citation
A protein–protein docking benchmark
Chen, R., Mintseris, J., Janin, J., & Weng, Z. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10390 · Cited by 345
Self-citation
A novel shape complementarity scoring function for protein‐protein docking
Chen, R., & Weng, Z. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10334 · Cited by 301
Self-citation

Flagged first, then by citations

Show all 31 references

Research works printed but not linked: 1

10.1002/(SICI)1097-0134(1997)1 <226::AID-PROT31>3.0.CO;2-O · DOI

Sorted by citations

Items 901–1,000 of 1,002

MutDock: A computational docking approach for fixed-backbone protein scaffold design
Chauhan, V. M., & Pantazes, R. J. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.933400 · Cited by 8
Molecular Simulation Study on the Interaction between Porcine CR1-like and C3b
Hou, Z., Yin, W., Hao, Z., Fan, K., Sun, N., Sun, P., & Li, H. (2023) · Molecules · doi:10.3390/molecules28052183 · Cited by 8
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network
Chen, Z. X., Liu, N., Huang, Y., Min, X., Zeng, X., Ge, S., Zhang, J., & Xia, N. (2023) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2023.3279019 · Cited by 8
Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques
Eshak, F., Pion, L., Scholler, P., Névoltris, D., Chames, P., Rondard, P., Pin, J., Acher, F., & Goupil-Lamy, A. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01620 · Cited by 9
Structural Models of Protein-DNA Complexes Based on Interface Prediction and Docking
Qin, S., & Zhou, H. (2011) · Current Protein and Peptide Science · doi:10.2174/138920311796957694 · Cited by 8
Preorientation of protein and RNA just before contacting
Guo, D., Liu, S., Huang, Y., & Xiao, Y. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.708604 · Cited by 8
Inferring protein-protein interactions in viral proteins by co-evolution of conserved side chains.
Wang, Y. E., & DeLisi, C. (2006) · PubMed · Cited by 8
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures
Guo, F., Li, S. C., Ma, W., & Wang, L. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2013.0069 · Cited by 8
Affinity Maturation by Semi-rational Approaches
Barderas, R., Desmet, J., Alard, P., & Casal, J. I. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-974-7_27 · Cited by 8
Determining Complex Structures using Docking Method with Single Particle Scattering Data
Wang, H., & Liu, H. (2017) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2017.00023 · Cited by 8
A structural perspective on the interactions of TRAF6 and B asigin during the onset of melanoma: A molecular dynamics simulation study
Biswas, R., Ghosh, S., & Bagchi, A. (2017) · Journal of Molecular Recognition · doi:10.1002/jmr.2643 · Cited by 8
Escape from humoral immunity is associated with treatment failure in HIV-1-infected patients receiving long-term antiretroviral therapy
Ouyang, Y., Yin, Q., Li, W., Li, Z., Kong, D., Wu, Y., Hong, K., Xing, H. Q., Shao, Y., Jiang, S., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-05594-5 · Cited by 9
Elucidating the precise interaction of reduced and oxidized states of Neuroglobin with Ubc12 and Cop9 using molecular mechanics studies
Suri, C., & Naik, P. K. (2012) · International Journal of Fundamental and Applied Sciences (IJFAS) · doi:10.59415/ijfas.v1i4.33 · Cited by 8
Co-precipitation molecules hemopexin and transferrin may be key molecules for fibrillogenesis in TTR V30M amyloidogenesis
Ohta, M., Sugano, A., Hatano, N., Sato, H., Shimada, H., Niwa, H., Sakaeda, T., Tei, H., Sakaki, Y., Yamamura, K., et al. (2017) · Transgenic Research · doi:10.1007/s11248-017-0054-x · Cited by 8
Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains
Biswas, A., Ghosh, S., Sinha, D., Dutta, A., Seal, S., Bagchi, A., & Sau, S. (2018) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2018.11.263 · Cited by 8
Screening, Identification, and Characterization of an Affinity Peptide Specific to MT1-MMP and Its Application in Tumor Imaging
Li, X., Ma, Z., Wang, H., Ren, L., Zhang, D., Liang, W., Zhang, G., Zhang, J., Yu, D., & Fang, X. (2019) · Bioconjugate Chemistry · doi:10.1021/acs.bioconjchem.9b00220 · Cited by 8
Novel conformation‐selective monoclonal antibodies against apoA‐I amyloid fibrils
Ohgita, T., Furutani, Y., Nakano, M., Hattori, M., Suzuki, A., Nakagawa, M., Naniwa, S., Morita, I., Oyama, H., Nishitsuji, K., et al. (2020) · FEBS Journal · doi:10.1111/febs.15487 · Cited by 8
Structural Perspective on Molecular Interaction of IgG and IgA with Spike and Envelope Proteins of SARS-CoV-2 and Its Implications to Non-Specific Immunity
(2020) · Biointerface Research in Applied Chemistry · doi:10.33263/briac113.1092310939 · Cited by 8
RosettaSurf—A surface-centric computational design approach
Scheck, A., Rosset, S., Defferrard, M., Loukas, A., Bonet, J., Vandergheynst, P., & Correia, B. E. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009178 · Cited by 8
Modeling of Membrane Proteins
Latek, D., Trzaskowski, B., Niewieczerzał, S., Miszta, P., Młynarczyk, K., Dębiński, A., Puławski, W., Yuan, S., Sztyler, A., Orzeł, U., et al. (2018) · Springer series on bio- and neurosystems · doi:10.1007/978-3-319-95843-9_12 · Cited by 8
Docking stability and electronic structure of azurin–cytochrome c551 complex system
Sugiyama, A., Takamatsu, Y., Nishikawa, K., Nagao, H., & Nishikawa, K. (2006) · International Journal of Quantum Chemistry · doi:10.1002/qua.21148 · Cited by 8
A structural perspective on protein?protein interactions
RUSSELL, R. (2004) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(04)00073-9 · Cited by 8
In silico‐designed novel non‐peptidic ABAD LD hot spot mimetics reverse Aβ‐induced mitochondrial impairments in vitro
Viswanath, A. N. I., Kim, T., Jung, S. Y., Lim, S. M., & Pae, A. N. (2017) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13065 · Cited by 8
Machine Learning-Driven Methods for Nanobody Affinity Prediction
Feng, H., Sun, X., Li, N., Xu, Q., Li, Q., Zhang, S., Xing, G., Zhang, G., & Wang, F. (2024) · ACS Omega · doi:10.1021/acsomega.4c09718 · Cited by 7
Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus
Bagchi, A., & Ghosh, T. C. (2011) · Journal of Biophysical Chemistry · doi:10.4236/jbpc.2011.24047 · Cited by 7
Anti-listerial peptides from a marine Bacillus velezensis FTL7: production optimization, characterizations and molecular docking studies
Johny, L. C., Kumar, B. S. G., Rao, S. J. A., & Suresh, P. V. (2024) · 3 Biotech · doi:10.1007/s13205-024-03944-5 · Cited by 7
Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies
Shang, W., Hu, X., Lin, X., Li, S., Xiong, S., Huang, B., & Wang, X. (2024) · Pharmaceuticals · doi:10.3390/ph17040424 · Cited by 8
A Novel Neuroprotective Derived Peptide of Erythropoietin Improved Cognitive Function in Vascular Dementia Mice
Zhou, Z., Ma, Y., Wu, T., Xu, T., Wu, S., Yang, G., Ding, J., & Wang, X. (2024) · Molecular Neurobiology · doi:10.1007/s12035-024-04639-x · Cited by 7
Molecular Computing and Residual Binding Mode in ERα and bZIP Proteins from Homo Sapiens: An Insight into the Signal Transduction in Breast Cancer Metastasis
Banerjee, A., & Ray, S. (2015) · Advances in intelligent systems and computing · doi:10.1007/978-81-322-2695-6_5 · Cited by 7
Development and Characterization of the Recombinant Human VEGF-EGF Dual-Targeting Fusion Protein as a Drug Delivery System
Li, J.-J., Lan, K.-L., Chang, S., Chen, Y.-F., Tsai, W.-C., Chiang, P.-H., Lin, M.-H., Fischer, W. B., Shih, Y.-S., Yen, S.-H., et al. (2015) · Bioconjugate Chemistry · doi:10.1021/acs.bioconjchem.5b00509 · Cited by 7
Decreased Activity of the Ghrhr and Gh Promoters Causes Dominantly Inherited GH Deficiency in Humanized GH1 Mouse Models
Ariyasu, D., Kubo, E., Higa, D., Shibata, S., Takaoka, Y., Sugimoto, M., Imaizumi, K., Hasegawa, T., & Araki, K. (2019) · Endocrinology · doi:10.1210/en.2019-00306 · Cited by 7
Methods and applications of machine learning in structure-based drug discovery
Sanjeevi, M., Hebbar, P. N., Aiswarya, N., Rashmi, S., Rahul, C. N., Mohan, A., Jeyakanthan, J., & Sekar, K. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90264-9.00025-8 · Cited by 8
DNAJB8 facilitates autophagic‐lysosomal degradation of viral Vif protein and restricts HIV ‐1 virion infectivity by rescuing APOBEC3G expression in host cells
Chand, K., Barman, M. K., Ghosh, P., & Mitra, D. (2023) · The FASEB Journal · doi:10.1096/fj.202201738r · Cited by 8
Binding Pattern Elucidation of NNK and NNAL Cigarette Smoke Carcinogens with NER Pathway Enzymes: an Onco-Informatics Study
Jamal, Q. M. S., Dhasmana, A., Lohani, M., Firdaus, S., Ansari, M. Y., Sahoo, G. C., & Haque, S. (2015) · Asian Pacific Journal of Cancer Prevention · doi:10.7314/apjcp.2015.16.13.5311 · Cited by 7
HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants
Gokhale, P., Sonawani, A., Idicula‐Thomas, S., Kerkar, S. C., Tongaonkar, H. B., & Mania‐Pramanik, J. (2014) · Journal of Medical Virology · doi:10.1002/jmv.23924 · Cited by 7
A holistic molecular docking approach for predicting protein-protein complex structure
Gong, X., Liu, B., Chang, S., Li, C., Chen, W., & Wang, C. (2010) · Science China Life Sciences · doi:10.1007/s11427-010-4050-0 · Cited by 7
Improved Isolation of Anti-rhTNF-α scFvs from Phage Display Library by Bioinformatics
Chen, W., Zhang, J., Zhang, T., Li, H., Wang, W., Xia, Z., & Wang, M. (2009) · Molecular Biotechnology · doi:10.1007/s12033-009-9172-x · Cited by 7
Targeting human secretory phospholipase A2 with designed peptide inhibitors for inflammatory therapy
Wang, P., Li, Y., Shao, Q., Zhou, W., & Wang, K. (2014) · Journal of drug targeting · doi:10.3109/1061186x.2014.959019 · Cited by 7
Using Graphics Processors to Accelerate Protein Docking Calculations
Ritchie, D. W., Venkatraman, V., & Mavridis, L. (2010) · Studies in health technology and informatics · doi:10.3233/978-1-60750-583-9-146 · Cited by 7
Belief Propagation Estimation of Protein and Domain Interactions Using the Sum–Product Algorithm
Morcos, F., Sikora, M., Alber, M., Kaiser, D., & Izaguirre, J. A. (2010) · IEEE Transactions on Information Theory · doi:10.1109/tit.2009.2037051 · Cited by 7
Using the concept of transient complex for affinity predictions in CAPRI rounds 20–27 and beyond
Qin, S., & Zhou, H. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24366 · Cited by 7
Structure‐based protein‐protein interaction networks and drug design
Naveed, H., & Han, J. J. (2013) · Quantitative Biology · doi:10.1007/s40484-013-0018-y · Cited by 8
ReplicOpter: A replicate optimizer for flexible docking
Demerdash, O., Buyan, A., & Mitchell, J. C. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22811 · Cited by 7
An ensemble docking calculation of lysozyme and HyHEL-10: Insight into the binding mechanism
Yamashita, T., & Takamatsu, Y. (2017) · AIP conference proceedings · doi:10.1063/1.5012301 · Cited by 7
Design and synthesis of BRC analogous peptides and their interactions with a key p53 peptide
Zhao, D., Lü, K., Liu, G., Ma, L., Zhu, H., & He, J. (2018) · FEBS Letters · doi:10.1002/1873-3468.13256 · Cited by 7
Cell-Free Expression of Sodium Channel Domains for Pharmacology Studies. Noncanonical Spider Toxin Binding Site in the Second Voltage-Sensing Domain of Human Nav1.4 Channel
Myshkin, M., Männikkö, R., Krumkacheva, O., Kulbatskii, D., Chugunov, A., Berkut, A., Paramonov, A., Shulepko, M., Fedin, M., Hanna, M., et al. (2019) · Frontiers in Pharmacology · doi:10.3389/fphar.2019.00953 · Cited by 5
VIRTUAL SCREENING STATEGIES IN DRUG DISCOVERY – A BRIEF OVERVIEW
Quân, P. M., & Pham, Q. L. (2021) · Vietnam Journal of Science and Technology/Science and Technology · doi:10.15625/2525-2518/59/4/16003 · Cited by 7
Unique Mechanism of the Interaction between Honey Bee Toxin TPNQ and rKir1.1 Potassium Channel Explored by Computational Simulations: Insights into the Relative Insensitivity of Channel towards Animal Toxins
Hu, J., Qiu, S., Yang, F., Cao, Z., Li, W., & Wu, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067213 · Cited by 7
Structural features and dynamics properties of human apolipoprotein A-I in a model of synthetic HDL
Rocco, A. G., Gianazza, E., Calabresi, L., Sensi, C., Franceschini, G., Sirtori, C. R., & Eberini, I. (2009) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2009.08.008 · Cited by 7
Optimization and dynamics of protein–protein complexes using B‐splines
Gillilan, R. E., & Lilien, R. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20088 · Cited by 7
Identification and functional characterization of the nuclear and nucleolar localization signals in the intrinsically disordered region of nucleomethylin
Shrikondawar, A. N., Chennoju, K., Ghosh, D. K., & Ranjan, A. (2024) · Journal of Cellular Physiology · doi:10.1002/jcp.31433 · Cited by 7
From Traditional Methods to Deep Learning Approaches: Advances in Protein–Protein Docking
Jiang, L., Zhang, K., Zhu, K., Zhang, H., Shen, C., & Hou, T. (2025) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.70016 · Cited by 6
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives
Qiu, L., & Zou, X. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103133 · Cited by 6
Stabilized D2R G protein-coupled receptor oligomers identify multi-state β-arrestin complexes
Sharrocks, K. L., Fanelli, F., Liu, Y., Milner, A. J., Yining, W., Byrne, B., & Hanyaloglu, A. C. (2025) · Nature Communications · doi:10.1038/s41467-025-64008-7 · Cited by 6
Engineered self-assembly of mucoadhesive Helicobacter pylori vaccines: CD4+ T cell-dependent immunity prevents bacterial colonization
Chen, X., Hao, J., Li, Y., Zou, Y., Li, A., Fan, Y., Ma, S.-J., Hao, S., Yu, S., Shen, D., et al. (2025) · Journal of Controlled Release · doi:10.1016/j.jconrel.2025.114417 · Cited by 6
Mechanism Analysis of Antimicrobial Peptide NoPv1 Related to Potato Late Blight through a Computer-Aided Study
Zhou, J.-S., Wen, H., & Yu, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25105312 · Cited by 6
Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality
Aftab, A., Sil, S., Nath, S., Basu, A., & Basu, S. (2024) · Journal of Molecular Evolution · doi:10.1007/s00239-024-10196-7 · Cited by 7
Molecular Docking and Virtual Screening to Investigate Lead Compounds for Veterinary Drug Development
Agrwal, A., Chadha, N., & Sahu, A. (2025) · Springer eBooks · doi:10.1007/978-981-97-7395-4_12 · Cited by 6
Modified β‐casein restores thermal reversibility of human carbonic anhydrase II: The salt bridge mechanism
Fallah‐Bagheri, A., Moosavi‐Movahedi, A. A., Taghizadeh, M. T., Khodarahmi‬, R., Ma’mani, L., Bijari, N., Bohlooli, M., Shafiee, A., Sheibani, N., & Saboury, A. A. (2013) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.1081 · Cited by 6
An insight into the interaction mode between CheB and chemoreceptor from two crystal structures of CheB methylesterase catalytic domain
Cho, K., Crane, B. R., & Park, S. (2011) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2011.06.090 · Cited by 6
Dockground scoring benchmarks for protein docking
Kotthoff, I., Kundrotas, P. J., & Vakser, I. A. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26306 · Cited by 6
Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation
Sonawani, A., Kharche, S., Dasgupta, D., & Sengupta, D. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.03.078 · Cited by 6
PLXND1-mediated calcium dyshomeostasis impairs endocardial endothelial autophagy in atrial fibrillation
Sun, M., Chen, Z. B., Song, Y., Zhang, B., Yang, J., & Tan, H. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.960480 · Cited by 6
Molecular Dynamics Simulation of the Antigen–Antibody Complex Formation Process between Hen Egg-White Lysozyme and HyHEL-10
Takamatsu, Y., Hamakubo, T., & Yamashita, T. (2022) · Bulletin of the Chemical Society of Japan · doi:10.1246/bcsj.20220239 · Cited by 6
A NR2E1‐interacting peptide of LSD1 inhibits the proliferation of brain tumour initiating cells
Hu, R., Hameed, U. F. S., Sun, X., Moorthy, B. S., Zhang, W., Jeffrey, P. D., Zhou, L. N., Ma, X., Chen, F., Pei, J., et al. (2022) · Cell Proliferation · doi:10.1111/cpr.13350 · Cited by 6
Structural neighboring property for identifying protein-protein binding sites
Guo, F., Li, S. C., Wei, Z., Zhu, D., Shen, C., & Wang, L. (2015) · BMC Systems Biology · doi:10.1186/1752-0509-9-s5-s3 · Cited by 6
Structural model of the Y-Family DNA polymerase V/RecA mutasome
Chandani, S., & Loechler, E. L. (2012) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2012.09.005 · Cited by 6
Structure-guided creation of AcAP5-derived and platelet targeted factor Xa inhibitors
Zhu, Y., Yuan, L., Liu, A., Shui, M., Li, R., Liu, X., Hu, W., & Wang, Y. (2015) · Biochemical Pharmacology · doi:10.1016/j.bcp.2015.04.004 · Cited by 6
Virtual Interactomics of Proteins from Biochemical Standpoint
Kubrycht, J., Sigler, K., & Souček, P. (2012) · Molecular Biology International · doi:10.1155/2012/976385 · Cited by 6
Isolation, Characterization, and Molecular Modeling of a Rheumatoid Factor from a Hepatitis C Virus Infected Patient with Sjögren’s Syndrome
Lee, Y., Tsai, K., Leu, S., Wang, T.-J., Liu, C.-Y., & Yang, Y. (2013) · The Scientific World JOURNAL · doi:10.1155/2013/516516 · Cited by 6
Predicting Protein Interactions by Brownian Dynamics Simulations
Meng, X.-Y., Xu, Y., Zhang, H., Mezei, M., & Cui, M. (2012) · BioMed Research International · doi:10.1155/2012/121034 · Cited by 6
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking
Su, C. T.-T., Nguyen, T.-D., Zheng, J., & Kwoh, C. K. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s16-s9 · Cited by 6
A compound‐based computational approach for the accurate determination of hot spots
Wang, L., Hou, Y., Quan, H., Xu, W., Bao, Y., Li, Y., Fu, Y., & Zou, S. (2013) · Protein Science · doi:10.1002/pro.2296 · Cited by 6
An in silico study of the effect of SOD1 electrostatic loop dynamics on amyloid‑like filament formation
Healy, E. F., & Cervantes, L. F. (2016) · European Biophysics Journal · doi:10.1007/s00249-016-1163-9 · Cited by 6
Structural insight, mutation and interactions in human Beta-catenin and SOX17 protein: A molecular-level outlook for organogenesis
Banerjee, A., & Ray, S. (2017) · Gene · doi:10.1016/j.gene.2017.01.026 · Cited by 6
Identification and characterization of loop7 motif and its role in regulating biological function of human APOBEC3G through molecular modeling and biological assay
Zhai, C., Ma, L., Zhang, Z., Ding, J., Wang, J., Zhang, Y., Li, X., Guo, F., Yu, L., Zhou, J., et al. (2017) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2017.05.002 · Cited by 6
A novel volumetric criterion for optimal shape matching of surfaces for protein-protein docking
Voruganti, H. K., & Dasgupta, B. (2017) · Journal of Computational Design and Engineering · doi:10.1016/j.jcde.2017.10.003 · Cited by 6
Prediction of protein oligomer structures using GALAXY in CASP13
Baek, M., Park, T., Woo, H., & Seok, C. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25814 · Cited by 6
Binding Mode of Human Norepinephrine Transporter Interacting with HIV-1 Tat
Adeniran, C. A., Yuan, Y., Davis, S. E., Lin, C., Xu, J., Zhu, J., & Zhan, C. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00792 · Cited by 6
Molten globule nature of Plasmodium falciparum P2 homo-tetramer
Mishra, P., Choudhary, S., Mukherjee, S., Sengupta, D., Sharma, S., & Hosur, R. V. (2015) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2015.03.010 · Cited by 6
Structural and Dynamic Insights into S100B Protein Activity Inhibition by Melittin for the Treatment of Epilepsy
Verma, N. K., Karmakar, M., Singh, K. P., & Smita, S. (2013) · Cited by 6
Identification of a conserved neutralizing epitope in the G-protein of Chandipura virus
Pavitrakar, D. V., Damle, R. G., Tripathy, A. S., & Shil, P. (2018) · Archives of Virology · doi:10.1007/s00705-018-3987-3 · Cited by 6
Data‐assisted protein structure modeling by global optimization in CASP12
Joo, K., Heo, S., Joung, I., Hong, S. H., Lee, S. J., & Lee, J. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25457 · Cited by 6
Design of Deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis
Obiero, J. M., & Sanders, D. A. R. (2011) · Protein Science · doi:10.1002/pro.635 · Cited by 6
Structure Prediction of Protein Complexes
Pierce, B. G., & Weng, Z. (2007) · Biological and medical physics series · doi:10.1007/978-0-387-68825-1_4 · Cited by 6
Self-citation
The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster
Heo, J., Ja, W. W., Benzer, S., & Goddard, W. A. (2008) · Biochemistry · doi:10.1021/bi801335p · Cited by 6
Molecular modeling of the complex between Torpedo acetylcholine receptor and anti-MIR Fab198
Konstantakaki, M., Tzartos, S. J., Poulas, K. A., & Eliopoulos, E. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.02.161 · Cited by 6
Protein–Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes
Wright, J. D., Sargsyan, K., Wu, X., Brooks, B. R., & Lim, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400508s · Cited by 6
Clustering protein-protein docking predictions
Tong, W., & Weng, Z. (2005) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/iembs.2004.1403850 · Cited by 6
Self-citation
Hierarchical, rotation-equivariant neural networks to predict the structure of protein complexesPreprint
Eismann, S., Townshend, R. J. L., Thomas, N., Jagota, M., Jing, B., & Dror, R. O. (2020) · arXiv (Cornell University) · Cited by 6
Docking, Scoring, and Virtual Screening in Drug Discovery
Spyrakis, F., Sarkar, A., & Kellogg, G. E. (2021) · Wiley eBooks · doi:10.1002/0471266949.bmc301 · Cited by 6
SHMT, SHMTML and PRPS1 synergize to regulate blood digestion and nutrient metabolism in Aedes aegypti mosquitoes
Pu, Q., Ren, H., Ou, Q., Yang, X., Wei, T., Zhao, L., Han, Y., Lou, Y., Kashyap, S., & Liu, S. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.143243 · Cited by 6
Generation of novel anti‐apo E monoclonal antibodies that selectively recognize apo E isoforms
Ohgita, T., Sakai, K., Fukui, N., Namba, N., Nakano, M., Kiguchi, Y., Morita, I., Oyama, H., Yamaki, K., Nagao, K., et al. (2024) · FEBS Letters · doi:10.1002/1873-3468.14858 · Cited by 5
KDM4C works in concert with GATA1 to regulate heme metabolism in head and neck squamous cell carcinoma
Wu, M.-C., Yang, S., Fang, W.-K., Chen, T.-J., Wu, C.-Y., Hsu, Y.-J., Shen, C.-E., Cheng, Y., Hsieh, W.-C., Yuh, C., et al. (2025) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-025-05693-x · Cited by 5
Bacterial Endophytes and arbuscular mycorrhizal fungi (AMF) Mitigate Marigold Mosaic Virus in Tagetes erecta via Antioxidant Enzyme Induction and Gene Regulation
Jha, Y., Kumari, A., Ghanaim, A. M., Sağlam, N. G., & Mohamed, H. I. (2025) · European Journal of Plant Pathology · doi:10.1007/s10658-025-03104-2 · Cited by 5
Purification of a Novel Anti-VEGFR2 Single Chain Antibody Fragmentand Evaluation of Binding Affinity by Surface Plasmon Resonance
Kordi, S., Rahmati‐Yamchi, M., Vostakolaei, M. A., Barzegari, A., & Abdolalizadeh, J. (2019) · Advanced Pharmaceutical Bulletin · doi:10.15171/apb.2019.008 · Cited by 5
Linear versus Branched Peptide with Same Amino Acid Sequence for Legumain‐Targeting in Macrophages: Targeting Efficiency and Bioimaging Potential
Kanathasan, J. S., Gunasagaram, D., Khan, S. U., Palanisamy, U. D., Radhakrishnan, A. K., Ahemad, N., & Swamy, V. (2020) · ChemistrySelect · doi:10.1002/slct.202002161 · Cited by 5
Development of Stable Chimeric IL-15 for Trans-Presentation by the Antigen Presenting Cells
Patidar, M., Yadav, N., & Dalai, S. K. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.646159 · Cited by 5
A computational framework for modeling functional protein‐protein interactions
Pal, A., Pal, D., & Mitra, P. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26156 · Cited by 5
Investigation of the Detailed AMPylated Reaction Mechanism for the Huntingtin Yeast-Interacting Protein E Enzyme HYPE
Liu, M., Huai, Z., Tan, H., & Chen, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22136999 · Cited by 5

Authors: Chen, R., Li, L., & Weng, Z.
Affiliations: Boston University (US)
Corresponding author: Weng, Zhiping
ORCID: Chen, Rong
Li, Li
Weng, Zhiping
Venue: Proteins: Structure, Function, and Bioinformatics
Publisher: Wiley
Published: 2003-05-14
Volume: 52
Issue: 1
Pages: 80-87
ISSN: 0887-3585 (ISSN-L)
1097-0134
DOI: 10.1002/prot.10389
OpenAlex: W2133712572
Cited by: 1,393
References: 31
Citations by year: 2026: 35 · 2025: 52 · 2024: 67 · 2023: 38 · 2022: 73 · 2021: 75 · 2020: 69 · 2019: 63 · 2018: 57 · 2017: 64 · 2016: 95 · 2015: 66 · 2014: 83 · 2013: 99 · 2012: 69
FWCI: 9.19
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Proteins Structure Function and Bioinformatics (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Cancer Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords: protein docking, scoring functions, ZDOCK, desolvation, electrostatics, antibody-antigen binding, conformational change
MeSH terms: Algorithms, Antibodies, Antigens, Binding Sites, Enzyme Inhibitors, Enzymes, Models, Molecular, Proteins, Protein Interaction Mapping, Macromolecular Substances, Static Electricity

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

ZDOCK: An initial‐stage protein‐docking algorithm

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks