Computational Design of Ligand Binding Proteins
暂无分享,去创建一个
[1] 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.
[2] Wei Wang,et al. Designing gene libraries from protein profiles for combinatorial protein experiments. , 2002, Nucleic acids research.
[3] Anna V. Hine,et al. ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons , 2013, Biochemical Society transactions.
[4] Frances H. Arnold,et al. Computational method to reduce the search space for directed protein evolution , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[5] Peer Bork,et al. SMART: recent updates, new developments and status in 2015 , 2014, Nucleic Acids Res..
[6] F. Ducastelle,et al. Generalized cluster description of multicomponent systems , 1984 .
[7] Manfred T Reetz,et al. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. , 2013, ACS synthetic biology.
[8] Manfred K. Warmuth,et al. Engineering proteinase K using machine learning and synthetic genes , 2007, BMC biotechnology.
[9] Frances H Arnold,et al. SCHEMA-guided protein recombination. , 2004, Methods in enzymology.
[10] Michael A. Saunders,et al. LSMR: An Iterative Algorithm for Sparse Least-Squares Problems , 2010, SIAM J. Sci. Comput..
[11] David Baker,et al. High-resolution comparative modeling with RosettaCM. , 2013, Structure.
[12] D. Segev,et al. Optimal codon randomization via mathematical programming. , 2013, Journal of theoretical biology.
[13] Liam J. McGuffin,et al. Intrinsic disorder prediction from the analysis of multiple protein fold recognition models , 2008, Bioinform..
[14] Christopher D. Snow,et al. SHARPEN—Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network , 2009, J. Comput. Chem..
[15] Margaret E. Johnson,et al. Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.
[16] J. Ponder,et al. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.
[17] Tanja Kortemme,et al. Flexible backbone sampling methods to model and design protein alternative conformations. , 2013, Methods in enzymology.
[18] Jenny J. Yang,et al. Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems. , 2013, Metallomics : integrated biometal science.
[19] Chris Bailey-Kellogg,et al. Optimization of Combinatorial Mutagenesis , 2011, RECOMB.
[20] Stephen L Mayo,et al. Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function , 2007, Proceedings of the National Academy of Sciences.
[21] E. Coutsias,et al. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling , 2009, Nature Methods.
[22] Yang Zhang,et al. I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.
[23] D. Baker,et al. RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design , 2011, PloS one.
[24] Costas D Maranas,et al. Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. , 2007, Protein engineering, design & selection : PEDS.
[25] Jeffrey B. Endelman,et al. Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450 , 2006, PLoS biology.
[26] Zukang Feng,et al. Ligand Depot: a data warehouse for ligands bound to macromolecules , 2004, Bioinform..
[27] Frances H Arnold,et al. A family of thermostable fungal cellulases created by structure-guided recombination , 2009, Proceedings of the National Academy of Sciences.
[28] Sereina Riniker,et al. Scents and sense: In silico perspectives on olfactory receptors , 2014, J. Comput. Chem..
[29] Adrian A Canutescu,et al. A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.
[30] Fei Zhou,et al. Ultra-Fast Evaluation of Protein Energies Directly from Sequence , 2006, PLoS Comput. Biol..
[31] Niles A Pierce,et al. Protein design is NP-hard. , 2002, Protein engineering.
[32] Gevorg Grigoryan,et al. Design of protein-interaction specificity affords selective bZIP-binding peptides , 2009, Nature.
[33] Xiong Wang,et al. Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers. , 2012, BioTechniques.
[34] Xiong Wang,et al. MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites. , 2014, BioTechniques.
[35] Rhiju Das,et al. Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz , 2012, PloS one.
[36] Anna V Hine,et al. Removing the redundancy from randomised gene libraries. , 2003, Journal of molecular biology.
[37] Liam J. McGuffin,et al. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction , 2011, Nucleic Acids Res..
[38] Gevorg Grigoryan,et al. Identifying and reducing error in cluster‐expansion approximations of protein energies , 2010, J. Comput. Chem..
[39] Christopher D. Snow,et al. Polarizable protein packing , 2011, J. Comput. Chem..
[40] Liam J McGuffin,et al. Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. , 2011, Methods.
[41] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[42] Chris Bailey-Kellogg,et al. Structure‐based design of combinatorial mutagenesis libraries , 2015, Protein science : a publication of the Protein Society.
[43] Lucas B Johnson,et al. Methods for library-scale computational protein design. , 2014, Methods in molecular biology.
[44] B. Kuhlman,et al. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming , 2014, Nucleic acids research.
[45] Gevorg Grigoryan,et al. Cluster expansion models for flexible‐backbone protein energetics , 2009, J. Comput. Chem..
[46] Philip A. Romero,et al. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. , 2010, Protein engineering, design & selection : PEDS.
[47] Adrian A Canutescu,et al. Cyclic coordinate descent: A robotics algorithm for protein loop closure , 2003, Protein science : a publication of the Protein Society.
[48] Frances H Arnold,et al. SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability* , 2009, The Journal of Biological Chemistry.
[49] Liam J. McGuffin,et al. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences , 2015, Nucleic Acids Res..
[50] Marco A Mena,et al. Automated design of degenerate codon libraries. , 2005, Protein engineering, design & selection : PEDS.
[51] Frances H Arnold,et al. A diverse set of family 48 bacterial glycoside hydrolase cellulases created by structure‐guided recombination , 2012, The FEBS journal.
[52] Eric Jones,et al. SciPy: Open Source Scientific Tools for Python , 2001 .
[53] Johan Desmet,et al. The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.
[54] 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.
[55] F. Arnold,et al. A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments , 2007, Nature Biotechnology.
[56] Wayne M Patrick,et al. User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. , 2003, Protein engineering.
[57] Daniel B. Roche,et al. Assessing the quality of modelled 3D protein structures using the ModFOLD server. , 2014, Methods in molecular biology.
[58] Stephen L. Mayo,et al. Dramatic performance enhancements for the FASTER optimization algorithm , 2006, J. Comput. Chem..
[59] Liam J McGuffin,et al. Structure and evolution of barley powdery mildew effector candidates , 2012, BMC Genomics.
[60] Mona Singh,et al. Solving and analyzing side-chain positioning problems using linear and integer programming , 2005, Bioinform..
[61] Gevorg Grigoryan,et al. Coarse-graining protein energetics in sequence variables. , 2005, Physical review letters.
[62] Frances H Arnold,et al. To whom correspondence should be addressed. , 2022 .