Hotspot-centric de novo design of protein binders.
暂无分享,去创建一个
David Baker | Sarel J Fleishman | John Karanicolas | Timothy A. Whitehead | Timothy A Whitehead | Jacob E Corn | Eva-Maria Strauch | D. Baker | J. Karanicolas | S. Fleishman | J. Corn | Eva-Maria Strauch | D. Baker
[1] Luhua Lai,et al. Nonnatural protein–protein interaction-pair design by key residues grafting , 2007, Proceedings of the National Academy of Sciences.
[2] Andreas Plückthun,et al. Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. , 2003, Journal of molecular biology.
[3] D. Eisenberg,et al. A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.
[4] Zhiping Weng,et al. ZRANK: Reranking protein docking predictions with an optimized energy function , 2007, Proteins.
[5] Z. Weng,et al. Protein–protein docking benchmark version 3.0 , 2008, Proteins.
[6] J. Shifman,et al. Triathlon for energy functions: Who is the winner for design of protein–protein interactions? , 2011, Proteins.
[7] A. Bogan,et al. Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.
[8] Gevorg Grigoryan,et al. Design of protein-interaction specificity affords selective bZIP-binding peptides , 2009, Nature.
[9] I. Wilson,et al. Crystal Structure of a Shark Single-Domain Antibody V Region in Complex with Lysozyme , 2004, Science.
[10] M. Eisenstein,et al. Computational mapping of anchoring spots on protein surfaces. , 2010, Journal of molecular biology.
[11] D C Richardson,et al. Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. , 1992, Biophysical journal.
[12] A. Plückthun,et al. Engineering novel binding proteins from nonimmunoglobulin domains , 2005, Nature Biotechnology.
[13] A. Braisted,et al. Minimizing a binding domain from protein A. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[14] Jens Meiler,et al. New algorithms and an in silico benchmark for computational enzyme design , 2006, Protein science : a publication of the Protein Society.
[15] A. Fersht,et al. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution. , 1994, Biochemistry.
[16] P. Harbury,et al. Automated design of specificity in molecular recognition , 2003, Nature Structural Biology.
[17] Andrzej Joachimiak,et al. High-throughput crystallography for structural genomics. , 2009, Current opinion in structural biology.
[18] Jeffrey J. Gray,et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.
[19] Burkhard Rost,et al. Protein–Protein Interaction Hotspots Carved into Sequences , 2007, PLoS Comput. Biol..
[20] Ruth Nussinov,et al. PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..
[21] A. Pommer,et al. Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. , 2000, Journal of molecular biology.
[22] T. Clackson,et al. A hot spot of binding energy in a hormone-receptor interface , 1995, Science.
[23] Jasmine L. Gallaher,et al. Alteration of enzyme specificity by computational loop remodeling and design , 2009, Proceedings of the National Academy of Sciences.
[24] R. Nussinov,et al. Conservation of polar residues as hot spots at protein interfaces , 2000, Proteins.
[25] A. Koide,et al. Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. , 2007, Methods in molecular biology.
[26] Z. Weng,et al. ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.
[27] T. Clackson,et al. Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. , 1998, Journal of molecular biology.
[28] D. Baker,et al. A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[29] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[30] Holger Gohlke,et al. DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions , 2010, Nucleic Acids Res..
[31] Leonard G. Presta,et al. Mapping of the C1q Binding Site on Rituxan, a Chimeric Antibody with a Human IgG1 Fc , 2000, The Journal of Immunology.
[32] A. Fersht,et al. Rapid, electrostatically assisted association of proteins , 1996, Nature Structural Biology.
[33] Andreas Plückthun,et al. Engineered proteins as specific binding reagents. , 2005, Current opinion in biotechnology.
[34] J A Wells,et al. Dissecting the energetics of an antibody‐antigen interface by alanine shaving and molecular grafting , 1994, Protein science : a publication of the Protein Society.
[35] G. Moore,et al. Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex. , 1995, Biochemistry.
[36] R. Nussinov,et al. Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[37] Collaborative Computational,et al. The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.
[38] C. E. Stebbins,et al. Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1. , 2000, Molecular cell.
[39] Jens Meiler,et al. RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite , 2011, PloS one.
[40] Jorge E. Galán,et al. Structural mimicry in bacterial virulence , 2001, Nature.
[41] David Baker,et al. A de novo protein binding pair by computational design and directed evolution. , 2011, Molecular cell.
[42] D. Baker,et al. Restricted sidechain plasticity in the structures of native proteins and complexes , 2011, Protein science : a publication of the Protein Society.
[43] Elisabeth L. Humphris,et al. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. , 2008, Structure.
[44] P. Chakrabarti,et al. Conservation and relative importance of residues across protein-protein interfaces , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[45] David E. Kim,et al. Computational Alanine Scanning of Protein-Protein Interfaces , 2004, Science's STKE.
[46] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[47] Timothy A. Whitehead,et al. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin , 2011, Science.
[48] A. Plückthun,et al. High-affinity binders selected from designed ankyrin repeat protein libraries , 2004, Nature Biotechnology.
[49] Gregory R. Hoffman,et al. Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP , 1998, Nature Structural Biology.
[50] Roland L. Dunbrack,et al. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains , 1994, Nature Structural Biology.
[51] Gira Bhabha,et al. Antibody Recognition of a Highly Conserved Influenza Virus Epitope , 2009, Science.
[52] D. Baker,et al. Role of conformational sampling in computing mutation‐induced changes in protein structure and stability , 2011, Proteins.
[53] H. Wolfson,et al. Shape complementarity at protein–protein interfaces , 1994, Biopolymers.
[54] S. Anderson,et al. Alanine Point-Mutations in the Reactive Region of Bovine Pancreatic Trypsin Inhibitor: Effects on the Kinetics and Thermodynamics of Binding to β-Trypsin and α-Chymotrypsin† , 1996 .
[55] E. Coutsias,et al. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling , 2009, Nature Methods.
[56] Gordon E. Moore,et al. Lithography and the future of Moore's law , 2006, Advanced Lithography.
[57] Sachdev S Sidhu,et al. Comprehensive and Quantitative Mapping of Energy Landscapes for Protein-Protein Interactions by Rapid Combinatorial Scanning*♦ , 2006, Journal of Biological Chemistry.
[58] D. Baker,et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.
[59] David Baker,et al. Motif‐directed flexible backbone design of functional interactions , 2009, Protein science : a publication of the Protein Society.
[60] David Baker,et al. Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.