Antibody humanization by structure-based computational protein design
暂无分享,去创建一个
Chris Bailey-Kellogg | Yoonjoo Choi | C. Bailey-Kellogg | M. Ackerman | Yoonjoo Choi | Casey K Hua | C. Sentman | Margaret E Ackerman | Casey Hua | Charles L Sentman
[1] Roland L. Dunbrack,et al. A new clustering of antibody CDR loop conformations. , 2011, Journal of molecular biology.
[2] Ming Lei,et al. Frontier of therapeutic antibody discovery: The challenges and how to face them. , 2012, World journal of biological chemistry.
[3] L. Presta,et al. Antibody Humanization Using Monovalent Phage Display* , 1997, The Journal of Biological Chemistry.
[4] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[5] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.
[6] Ming-Ru Wu,et al. An NKp30-Based Chimeric Antigen Receptor Promotes T Cell Effector Functions and Antitumor Efficacy In Vivo , 2012, The Journal of Immunology.
[7] S. Batra,et al. Effects of humanization and gene shuffling on immunogenicity and antigen binding of anti‐tag‐72 single‐chain Fvs , 2001, International journal of cancer.
[8] T. Ohta,et al. Population Biology of Antigen Presentation by MHC Class I Molecules , 1996, Science.
[9] Chris Bailey-Kellogg,et al. A divide‐and‐conquer approach to determine the Pareto frontier for optimization of protein engineering experiments , 2012, Proteins.
[10] Noreen R. Gonzales,et al. SDR grafting of a murine antibody using multiple human germline templates to minimize its immunogenicity. , 2004, Molecular immunology.
[11] Andrew C. R. Martin,et al. The humanness of macaque antibody sequences. , 2010, Journal of molecular biology.
[12] W. C. Still,et al. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .
[13] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[14] M. Clark,et al. Antibody humanization: a case of the 'Emperor's new clothes'? , 2000, Immunology today.
[15] C. Deane,et al. ABangle: characterising the VH-VL orientation in antibodies. , 2013, Protein engineering, design & selection : PEDS.
[16] D. Baker,et al. Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes , 2014, Proceedings of the National Academy of Sciences.
[17] Amy C. Anderson,et al. Computational structure-based redesign of enzyme activity , 2009, Proceedings of the National Academy of Sciences.
[18] A. Younes,et al. A phase 1 dose‐escalation study of XmAb®2513 in patients with relapsed or refractory Hodgkin lymphoma , 2015, British journal of haematology.
[19] Vibha Jawa,et al. T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation. , 2013, Clinical immunology.
[20] Bruce Randall Donald,et al. Protein Design Using Continuous Rotamers , 2012, PLoS Comput. Biol..
[21] A. Lesk,et al. Conformations of immunoglobulin hypervariable regions , 1989, Nature.
[22] H. Steven Wiley,et al. Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library , 2003, Nature Biotechnology.
[23] J. Foote,et al. Immunogenicity of engineered antibodies. , 2005, Methods.
[24] C. Deane,et al. CODA: A combined algorithm for predicting the structurally variable regions of protein models , 2001, Protein science : a publication of the Protein Society.
[25] P. T. Jones,et al. Replacing the complementarity-determining regions in a human antibody with those from a mouse , 1986, Nature.
[26] P. Carter. Potent antibody therapeutics by design , 2006, Nature Reviews Immunology.
[27] Thomas Singer,et al. The safety and side effects of monoclonal antibodies , 2010, Nature Reviews Drug Discovery.
[28] Paolo Marcatili,et al. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server , 2013, Bioinform..
[29] Etienne Weiss,et al. Therapeutic antibodies: successes, limitations and hopes for the future , 2009, British journal of pharmacology.
[30] E. Reinherz,et al. Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. , 2003, Journal of molecular biology.
[31] A. Lesk,et al. Standard conformations for the canonical structures of immunoglobulins. , 1997, Journal of molecular biology.
[32] Jeffrey J. Gray,et al. Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking , 2009, Proteins.
[33] Chris Bailey-Kellogg,et al. Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate , 2014, Cellular and Molecular Life Sciences.
[34] Marie-Paule Lefranc,et al. IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor VJ and VDJrearrangement analysis , 2004, Nucleic Acids Res..
[35] Brian D. Weitzner,et al. Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization , 2014, Proteins.
[36] Charlotte M Deane,et al. Predicting antibody complementarity determining region structures without classification. , 2011, Molecular bioSystems.
[37] Chris Bailey-Kellogg,et al. Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate , 2015, PLoS Comput. Biol..
[38] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[39] Yoonjoo Choi,et al. FREAD revisited: Accurate loop structure prediction using a database search algorithm , 2010, Proteins.
[40] Benjamin D. Sellers,et al. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. , 2009, Journal of molecular biology.
[41] Yanay Ofran,et al. Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure , 2012, Nucleic Acids Res..
[42] Chris Bailey-Kellogg,et al. Structure-Guided Deimmunization of Therapeutic Proteins , 2012, RECOMB.
[43] G. Winter,et al. Antibody framework residues affecting the conformation of the hypervariable loops. , 1992, Journal of molecular biology.
[44] R. Dubridge,et al. The immunogenicity of humanized and fully human antibodies , 2010, mAbs.
[45] Ida Retter,et al. VBASE2, an integrative V gene database , 2004, Nucleic Acids Res..
[46] Chris Bailey-Kellogg,et al. Protein deimmunization via structure‐based design enables efficient epitope deletion at high mutational loads , 2015, Biotechnology and bioengineering.
[47] J. Reichert,et al. Development trends for human monoclonal antibody therapeutics , 2010, Nature Reviews Drug Discovery.
[48] N. Lonberg,et al. Human Monoclonal Antibodies from Transgenic Mice , 2008, Handbook of experimental pharmacology.
[49] Donald Hilvert,et al. De novo enzymes by computational design. , 2013, Current opinion in chemical biology.
[50] Uwe T Bornscheuer,et al. Finding better protein engineering strategies. , 2009, Nature chemical biology.
[51] M. Berger,et al. Human antibodies for immunotherapy development generated via a human B‐cell hybridoma technology , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[52] Sebastian Kelm,et al. Fragment‐based modeling of membrane protein loops: Successes, failures, and prospects for the future , 2014, Proteins.
[53] Jan Brezovsky,et al. Computational tools for designing and engineering enzymes. , 2014, Current opinion in chemical biology.
[54] François Ehrenmann,et al. IMGT/3Dstructure-DB: querying the IMGT database for 3D structures in immunology and immunoinformatics (IG or antibodies, TR, MH, RPI, and FPIA). , 2011, Cold Spring Harbor protocols.
[55] Herren Wu,et al. Antibody humanization by framework shuffling. , 2005, Methods.
[56] R. Goldstein. Efficient rotamer elimination applied to protein side-chains and related spin glasses. , 1994, Biophysical journal.
[57] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[58] Paolo Marcatili,et al. PIGS: automatic prediction of antibody structures , 2008, Bioinform..
[59] A. Lesk,et al. Canonical structures for the hypervariable regions of immunoglobulins. , 1987, Journal of molecular biology.
[60] Anna Tramontano,et al. Tabhu: tools for antibody humanization , 2015, Bioinform..
[61] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[62] A. Adler,et al. Monoclonal antibody humanness score and its applications , 2013, BMC Biotechnology.
[63] G. Winter,et al. Phage antibodies: filamentous phage displaying antibody variable domains , 1990, Nature.
[64] A R Rees,et al. Humanization of murine monoclonal antibodies through variable domain resurfacing. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[65] M. Dennis. CDR Repair: A Novel Approach to Antibody Humanization , 2010 .
[66] Andrew C. R. Martin,et al. Analyzing the "degree of humanness" of antibody sequences. , 2007, Journal of molecular biology.
[67] Haruki Nakamura,et al. High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations , 2014, Proteins.
[68] B. Bogen,et al. Review: To What Extent are T Cells Tolerant to Immunoglobulin Variable Regions? , 2009, Scandinavian journal of immunology.
[69] David Baker,et al. Removing T-cell epitopes with computational protein design , 2014, Proceedings of the National Academy of Sciences.
[70] Andrew C. R. Martin,et al. Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. , 2008, Molecular immunology.
[71] N. Bradley,et al. A novel platform to produce human monoclonal antibodies , 2011, mAbs.
[72] Hans-Georg Rammensee,et al. MHC ligands and peptide motifs: first listing , 2004, Immunogenetics.
[73] A. Speak,et al. Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery , 2014, Nature Biotechnology.
[74] J. Osbourn,et al. From rodent reagents to human therapeutics using antibody guided selection. , 2005, Methods.
[75] Roland L. Dunbrack,et al. proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .
[76] G. A. Lazar,et al. A molecular immunology approach to antibody humanization and functional optimization. , 2007, Molecular immunology.
[77] G. Alter,et al. Highly parallel characterization of IgG Fc binding interactions , 2014, mAbs.
[78] Richard Friesner,et al. Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction , 2014, Proteins.
[79] J. C. Almagro,et al. Use of human germline genes in a CDR homology-based approach to antibody humanization. , 2005, Methods.
[80] S. Farajnia,et al. Antibody humanization methods – a review and update , 2013, Biotechnology & genetic engineering reviews.