Jastrzebski M
Methods Mol Biol. 2024; 2780:327-343.
PMID: 38987476
DOI: 10.1007/978-1-0716-3985-6_17.
Sonawani A, Naglekar A, Kharche S, Sengupta D
Methods Mol Biol. 2024; 2780:257-280.
PMID: 38987472
DOI: 10.1007/978-1-0716-3985-6_13.
Kuder K
Methods Mol Biol. 2024; 2780:3-14.
PMID: 38987460
DOI: 10.1007/978-1-0716-3985-6_1.
Dequeker C, Mohseni Behbahani Y, David L, Laine E, Carbone A
PLoS Comput Biol. 2022; 18(1):e1009825.
PMID: 35089918
PMC: 8827487.
DOI: 10.1371/journal.pcbi.1009825.
Sunny S, Jayaraj P
Protein J. 2021; 41(1):1-26.
PMID: 34787783
DOI: 10.1007/s10930-021-10031-8.
Coarse-grained (hybrid) integrative modeling of biomolecular interactions.
Roel-Touris J, Bonvin A
Comput Struct Biotechnol J. 2020; 18:1182-1190.
PMID: 32514329
PMC: 7264466.
DOI: 10.1016/j.csbj.2020.05.002.
The HDOCK server for integrated protein-protein docking.
Yan Y, Tao H, He J, Huang S
Nat Protoc. 2020; 15(5):1829-1852.
PMID: 32269383
DOI: 10.1038/s41596-020-0312-x.
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK.
Roel-Touris J, Don C, Honorato R, Rodrigues J, Bonvin A
J Chem Theory Comput. 2019; 15(11):6358-6367.
PMID: 31539250
PMC: 6854652.
DOI: 10.1021/acs.jctc.9b00310.
Molecular Docking: Shifting Paradigms in Drug Discovery.
Pinzi L, Rastelli G
Int J Mol Sci. 2019; 20(18).
PMID: 31487867
PMC: 6769923.
DOI: 10.3390/ijms20184331.
HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.
He J, Wang J, Tao H, Xiao Y, Huang S
Nucleic Acids Res. 2019; 47(W1):W35-W42.
PMID: 31114906
PMC: 6602492.
DOI: 10.1093/nar/gkz412.
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry.
Yan Y, Tao H, Huang S
Nucleic Acids Res. 2018; 46(W1):W423-W431.
PMID: 29846641
PMC: 6030965.
DOI: 10.1093/nar/gky398.
Efficient flexible backbone protein-protein docking for challenging targets.
Marze N, Roy Burman S, Sheffler W, Gray J
Bioinformatics. 2018; 34(20):3461-3469.
PMID: 29718115
PMC: 6184633.
DOI: 10.1093/bioinformatics/bty355.
Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.
Yan Y, Wen Z, Zhang D, Huang S
Nucleic Acids Res. 2018; 46(9):e56.
PMID: 29506237
PMC: 5961370.
DOI: 10.1093/nar/gky113.
Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures.
Kim J, Chirikjian G
J Comput Biol. 2017; 25(1):72-88.
PMID: 29172668
PMC: 5757073.
DOI: 10.1089/cmb.2017.0166.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Yan Y, Zhang D, Zhou P, Li B, Huang S
Nucleic Acids Res. 2017; 45(W1):W365-W373.
PMID: 28521030
PMC: 5793843.
DOI: 10.1093/nar/gkx407.
Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors.
Bartuzi D, Kaczor A, Targowska-Duda K, Matosiuk D
Molecules. 2017; 22(2).
PMID: 28241450
PMC: 6155844.
DOI: 10.3390/molecules22020340.
Computing the Dynamic Supramolecular Structural Proteome.
Nussinov R, Papin J, Vakser I
PLoS Comput Biol. 2017; 13(1):e1005290.
PMID: 28103234
PMC: 5245783.
DOI: 10.1371/journal.pcbi.1005290.
Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.
Xu X, Qiu L, Yan C, Ma Z, Grinter S, Zou X
Proteins. 2016; 85(3):424-434.
PMID: 27802576
PMC: 5313341.
DOI: 10.1002/prot.25203.
Molecular docking as a popular tool in drug design, an in silico travel.
de Ruyck J, Brysbaert G, Blossey R, Lensink M
Adv Appl Bioinform Chem. 2016; 9:1-11.
PMID: 27390530
PMC: 4930227.
DOI: 10.2147/AABC.S105289.
Protein docking with predicted constraints.
Krippahl L, Barahona P
Algorithms Mol Biol. 2015; 10:9.
PMID: 25722738
PMC: 4340843.
DOI: 10.1186/s13015-015-0036-6.