Integrating linear optimization with structural modeling to increase HIV neutralization breadth
暂无分享,去创建一个
Jens Meiler | Yevgeniy Vorobeychik | James E. Crowe | Swetasudha Panda | Alexander M. Sevy | J. Meiler | J. Crowe | A. M. Sevy | Swetasudha Panda | Yevgeniy Vorobeychik
[1] A. Sandelin,et al. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. , 2004, Journal of molecular biology.
[2] Chris Bailey-Kellogg,et al. Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models , 2015, J. Comput. Biol..
[3] Timothy A. Whitehead,et al. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin , 2011, Science.
[4] Roberto A Chica,et al. Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles , 2014, Proteins.
[5] Chih-Jen Lin,et al. LIBLINEAR: A Library for Large Linear Classification , 2008, J. Mach. Learn. Res..
[6] Young Do Kwon,et al. Residue-Level Prediction of HIV-1 Antibody Epitopes Based on Neutralization of Diverse Viral Strains , 2013, Journal of Virology.
[7] Samuel L. DeLuca,et al. Human Germline Antibody Gene Segments Encode Polyspecific Antibodies , 2013, PLoS Comput. Biol..
[8] Andrew Leaver-Fay,et al. Resource Computationally Designed Bispecific Antibodies using Negative State Repertoires Graphical Abstract Highlights , 2016 .
[9] Jens Meiler,et al. Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth. , 2015, The Journal of clinical investigation.
[10] S. L. Mayo,et al. De novo protein design: fully automated sequence selection. , 1997, Science.
[11] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[12] Jack Snoeyink,et al. Scientific benchmarks for guiding macromolecular energy function improvement. , 2013, Methods in enzymology.
[13] Jens Meiler,et al. Protocols for Molecular Modeling with Rosetta3 and RosettaScripts , 2016, Biochemistry.
[14] Pham Phung,et al. Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target , 2009, Science.
[15] Tongqing Zhou,et al. Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01 , 2010, Science.
[16] D. Baker,et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.
[17] Colin A. Smith,et al. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. , 2008, Journal of molecular biology.
[18] Jens Meiler,et al. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences , 2015, PLoS Comput. Biol..
[19] D. Baker,et al. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.
[20] P. Harbury,et al. Automated design of specificity in molecular recognition , 2003, Nature Structural Biology.
[21] Tongqing Zhou,et al. Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization , 2013, Science.
[22] Tongqing Zhou,et al. Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization , 2013, Cell.
[23] Alex Nisthal,et al. Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles , 2010, Proceedings of the National Academy of Sciences.
[24] Julia M. Shifman,et al. Modulating calmodulin binding specificity through computational protein design. , 2002, Journal of molecular biology.
[25] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[26] Andrew Leaver-Fay,et al. Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface , 2014, Nature Biotechnology.
[27] D. Baker,et al. Elicitation of structure-specific antibodies by epitope scaffolds , 2010, Proceedings of the National Academy of Sciences.
[28] Rodrigo Lopez,et al. Clustal W and Clustal X version 2.0 , 2007, Bioinform..
[29] Doyle P. Bean,et al. Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases. , 2014, Structure.
[30] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[31] Young Do Kwon,et al. Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. , 2013, Immunity.
[32] David Baker,et al. Computational design of trimeric influenza neutralizing proteins targeting the hemagglutinin receptor binding site , 2017, Nature Biotechnology.
[33] Baoshan Zhang,et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody , 2012, Nature.
[34] Corinna Cortes,et al. Support-Vector Networks , 1995, Machine Learning.
[35] Ron Diskin,et al. Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding , 2011, Science.
[36] Andrew Leaver-Fay,et al. A Generic Program for Multistate Protein Design , 2011, PloS one.
[37] Brian Kuhlman,et al. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins , 2014, Proceedings of the National Academy of Sciences.
[38] David Baker,et al. Proof of principle for epitope-focused vaccine design , 2014, Nature.
[39] Young Do Kwon,et al. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection , 2015, Cell.
[40] Mario Roederer,et al. Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 , 2010, Science.
[41] David Nemazee,et al. Rational immunogen design to target specific germline B cell receptors , 2012, Retrovirology.
[42] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[43] Samuel L. DeLuca,et al. Small-molecule ligand docking into comparative models with Rosetta , 2013, Nature Protocols.
[44] Ron Diskin,et al. Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design , 2011, Science.