In Silico Aptamer Docking Studies: From a Retrospective Validation to a Prospective Case Study'TIM3 Aptamers Binding
Tóm tắt
Từ khóa
Tài liệu tham khảo
Lee, 2005, A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165, Proc Natl Acad Sci USA, 102, 18902, 10.1073/pnas.0509069102
Soldevilla, 2015, 2-fluoro-RNA oligonucleotide CD40 targeted aptamers for the control of B lymphoma and bone-marrow aplasia, Biomaterials, 67, 274, 10.1016/j.biomaterials.2015.07.020
Pastor, 2013, CD28 aptamers as powerful immune response modulators, Mol Ther Nucleic Acids, 2, e98, 10.1038/mtna.2013.26
Hodi, 2010, Improved survival with ipilimumab in patients with metastatic melanoma, N Engl J Med, 363, 711, 10.1056/NEJMoa1003466
Topalian, 2012, Safety, activity, and immune correlates of anti-PD-1 antibody in cancer, N Engl J Med, 366, 2443, 10.1056/NEJMoa1200690
Pardoll, 2012, The blockade of immune checkpoints in cancer immunotherapy, Nat Rev Cancer, 12, 252, 10.1038/nrc3239
Hervas-Stubbs, 2016, Identification of TIM3 2'-fluoro oligonucleotide aptamer by HT-SELEX for cancer immunotherapy, Oncotarget, 7, 4522, 10.18632/oncotarget.6608
Puton, 2012, Computational methods for prediction of protein-RNA interactions, J Struct Biol, 179, 261, 10.1016/j.jsb.2011.10.001
Tuszynska, 2014, Computational modeling of protein-RNA complex structures, Methods, 65, 310, 10.1016/j.ymeth.2013.09.014
Guilhot-Gaudeffroy, 2014, Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities, PLoS One, 9, e108928, 10.1371/journal.pone.0108928
Huang, 2013, A novel protocol for three-dimensional structure prediction of RNA-protein complexes, Sci Rep, 3, 1887, 10.1038/srep01887
Perez-cano, 2010, Structural Prediction of protein-rna interaction by computational docking with propensity-based statistical potentials, Pac Symp Biocomput, 293
Li, 2012, A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys, Proteins, 80, 14, 10.1002/prot.23117
Tuszynska, 2011, DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking, BMC Bioinformatics, 12, 348, 10.1186/1471-2105-12-348
Olega, 2010, Software news and update autodock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem, 31, 455, 10.1002/jcc.21334
de Vries, 2010, The HADDOCK web server for data-driven biomolecular docking, Nat Protoc, 5, 883, 10.1038/nprot.2010.32
Huang, 2010, MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19, Proteins, 78, 3096, 10.1002/prot.22797
Schneidman-Duhovny, 2005, PatchDock and SymmDock: servers for rigid and symmetric docking, Nucleic Acids Res, 33, W363, 10.1093/nar/gki481
Ahirwar, 2016, In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules, Sci Rep, 6, 21285, 10.1038/srep21285
Hu, 2015, Computational selection of RNA aptamer against angiopoietin-2 and experimental evaluation, Biomed Res Int, 2015, 658712, 10.1155/2015/658712
Lao, 2014, Selection of aptamers targeting the sialic acid receptor of hemagglutinin by epitope-specific SELEX, Chem Commun (Camb), 50, 8719, 10.1039/C4CC03116D
Baig, 2015, Development of ssDNA aptamers as potent inhibitors of Mycobacterium tuberculosis acetohydroxyacid synthase, Biochim Biophys Acta, 1854, 1338, 10.1016/j.bbapap.2015.05.003
Oliviero, 2016, Screening platform toward new anti-HIV aptamers set on molecular docking and fluorescence quenching techniques, Anal Chem, 88, 2327, 10.1021/acs.analchem.5b04268
Tseng, 2011, Entropic fragment-based approach to aptamer design, Chem Biol Drug Des, 78, 1, 10.1111/j.1747-0285.2011.01125.x
Shcherbinin, 2015, Computer-aided design of aptamers for cytochrome p450, J Struct Biol, 191, 112, 10.1016/j.jsb.2015.07.003
Pérez-Cano, 2012, A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data, Proteins, 80, 1872, 10.1002/prot.24075
Rockey, 2011, Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling, Nucleic Acid Ther, 21, 299, 10.1089/nat.2011.0313
Zhou, 2015, Searching the sequence space for potent aptamers using SELEX in Silico, J Chem Theory Comput, 11, 5939, 10.1021/acs.jctc.5b00707
Hoinka, 2015, Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery, Nucleic Acids Res, 43, 5699, 10.1093/nar/gkv308
Luo, 2010, Computational approaches toward the design of pools for the in vitro selection of complex aptamers, RNA, 16, 2252, 10.1261/rna.2102210
Tesmer, 2012, Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer, Structure, 20, 1300, 10.1016/j.str.2012.05.002
Huang, 2003, Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer, Proc Natl Acad Sci USA, 100, 9268, 10.1073/pnas.1632011100
Davlieva, 2014, Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis, Nucleic Acids Res, 42, 10795, 10.1093/nar/gku743
Padlan, 2014, An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates, RNA, 20, 447, 10.1261/rna.043034.113
Chimnaronk, 2009, Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon, Biochemistry, 48, 5057, 10.1021/bi900337d
Berendsen, 1995, GROMACS: A message-passing parallel molecular dynamics implementation, Comput. Phys. Commun, 91, 43, 10.1016/0010-4655(95)00042-E
Reuter, 2010, RNAstructure: software for RNA secondary structure prediction and analysis, BMC Bioinformatics, 11, 129, 10.1186/1471-2105-11-129
Das, 2007, Automated de novo prediction of native-like RNA tertiary structures, Proc Natl Acad Sci USA, 104, 14664, 10.1073/pnas.0703836104
Cheng, 2015, Modeling complex RNA tertiary folds with Rosetta, Methods Enzymol, 553, 35, 10.1016/bs.mie.2014.10.051
Das, 2010, Atomic accuracy in predicting and designing noncanonical RNA structure, Nat Methods, 7, 291, 10.1038/nmeth.1433
Hermann, 2000, Adaptive recognition by nucleic acid aptamers, Science, 287, 820, 10.1126/science.287.5454.820
Deng, 2004, Structural Interaction Fingerprint (SIFt): a novel method for analyzing three-dimensional protein − ligand binding interactions Structural Interaction Fingerprint (SIFt): a novel method for analyzing, J Med Chem, 47, 337, 10.1021/jm030331x
Pérez-Nueno, 2009, APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening, J Chem Inf Model, 49, 1245, 10.1021/ci900043r
Cao, 2007, T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface, Immunity, 26, 311, 10.1016/j.immuni.2007.01.016
Zhu, 2005, The Tim-3 ligand galectin-9 negatively regulates T helper type 1 immunity, Nat Immunol, 6, 1245, 10.1038/ni1271
Huang, 2015, CEACAM1 regulates TIM-3-mediated tolerance and exhaustion, Nature, 517, 386, 10.1038/nature13848
Wang, 2001, How does consensus scoring work for virtual library screening? An idealized computer experiment, J Chem Inf Comput Sci, 41, 1422, 10.1021/ci010025x
Ballante, 2016, An automated strategy for binding-pose selection and docking assessment in structure-based drug design, J Chem Inf Model, 56, 54, 10.1021/acs.jcim.5b00603