Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data.
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[1] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[2] T S Baker,et al. Low resolution meets high: towards a resolution continuum from cells to atoms. , 1996, Current opinion in structural biology.
[3] K. Schulten,et al. Self-organizing neural networks bridge the biomolecular resolution gap. , 1998, Journal of molecular biology.
[4] J. Lepault,et al. Electronic Reprint Biological Crystallography on the Fitting of Model Electron Densities into Em Reconstructions: a Reciprocal-space Formulation , 2022 .
[5] Sandor Vajda,et al. CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.
[6] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[7] R. Abagyan,et al. Identification of protein-protein interaction sites from docking energy landscapes. , 2004, Journal of molecular biology.
[8] Rolf Boelens,et al. Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility , 2006, Nucleic acids research.
[9] Alexandre M J J Bonvin,et al. HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets , 2007, Proteins.
[10] A. Brunger. Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.
[11] Stefan Birmanns,et al. Multi-resolution anchor-point registration of biomolecular assemblies and their components. , 2007, Journal of structural biology.
[12] Conrad C. Huang,et al. Visualizing density maps with UCSF Chimera. , 2007, Journal of structural biology.
[13] Christopher L. McClendon,et al. Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.
[14] A. Fersht,et al. Structure–function–rescue: the diverse nature of common p53 cancer mutants , 2007, Oncogene.
[15] Niels Volkmann,et al. Density-based score for selecting near-native atomic models of unknown structures. , 2007, Journal of structural biology.
[16] Zhili Xu,et al. A conserved rRNA methyltransferase regulates ribosome biogenesis , 2008, Nature Structural &Molecular Biology.
[17] Frank Alber,et al. Integrating diverse data for structure determination of macromolecular assemblies. , 2008, Annual review of biochemistry.
[18] Ben M. Webb,et al. Protein structure fitting and refinement guided by cryo-EM density. , 2008, Structure.
[19] T. Kawabata. Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model , 2008, Biophysical journal.
[20] A. Bonvin,et al. The HADDOCK web server for data-driven biomolecular docking , 2010, Nature Protocols.
[21] Zhiping Weng,et al. Protein–protein docking benchmark version 4.0 , 2010, Proteins.
[22] Alexandre M J J Bonvin,et al. Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions , 2010, Proteins.
[23] Pedro Alexandrino Fernandes,et al. Protein–protein docking dealing with the unknown , 2009, J. Comput. Chem..
[24] Alexandre M. J. J. Bonvin,et al. Building Macromolecular Assemblies by Information-driven Docking , 2010, Molecular & Cellular Proteomics.
[25] Min Xu,et al. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps , 2010, Bioinform..
[26] H. Wolfson,et al. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map , 2010, Proteins.
[27] Jianlin Lei,et al. Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy , 2011, Proceedings of the National Academy of Sciences.
[28] Alexandre M J J Bonvin,et al. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. , 2011, Structure.
[29] E. Orlova,et al. Structural Analysis of Macromolecular Assemblies by Electron Microscopy , 2011, Chemical reviews.
[30] Daisuke Kihara,et al. Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. , 2012, The journal of physical chemistry. B.
[31] Hong Liang,et al. A method for integrative structure determination of protein-protein complexes , 2012, Bioinform..
[32] Martin Zacharias,et al. ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps , 2012, PloS one.
[33] M. S. Chapman,et al. Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. , 2012, Virology.
[34] Andrej Sali,et al. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images , 2012, Proceedings of the National Academy of Sciences.
[35] Daniel Boehringer,et al. Structural Insights into Methyltransferase KsgA Function in 30S Ribosomal Subunit Biogenesis* , 2012, The Journal of Biological Chemistry.
[36] Michael Levitt,et al. Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex , 2013, Science.
[37] J. Carrascosa,et al. Large Terminase Conformational Change Induced by Connector Binding in Bacteriophage T7* , 2013, The Journal of Biological Chemistry.
[38] A. Bonvin,et al. On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. , 2013, Acta crystallographica. Section D, Biological crystallography.
[39] M. Rossmann,et al. Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody , 2013, Journal of Virology.
[40] David W Ritchie,et al. gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration. , 2013, Journal of structural biology.
[41] P. Aloy,et al. Interactome3D: adding structural details to protein networks , 2013, Nature Methods.
[42] Alexandre M J J Bonvin,et al. Advances in integrative modeling of biomolecular complexes. , 2013, Methods.
[43] Daisuke Kihara,et al. Computational methods for constructing protein structure models from 3D electron microscopy maps. , 2013, Journal of structural biology.
[44] Alexandre M. J. J. Bonvin,et al. A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking , 2013, PloS one.
[45] Jerome Wielens,et al. Oncogenic protein interfaces: small molecules, big challenges , 2014, Nature Reviews Cancer.
[46] Sheng-You Huang,et al. Search strategies and evaluation in protein-protein docking: principles, advances and challenges. , 2014, Drug discovery today.
[47] Barry Honig,et al. Structural bioinformatics of the interactome. , 2014, Annual review of biophysics.
[48] K. Lage. Protein-protein interactions and genetic diseases: The interactome. , 2014, Biochimica et biophysica acta.
[49] J. Rodrigues,et al. Integrative computational modeling of protein interactions , 2014, The FEBS journal.