Rational evolutionary design: the theory of in vitro protein evolution.

[1]  K N Houk,et al.  Evolution of shape complementarity and catalytic efficiency from a primordial antibody template. , 1999, Science.

[2]  Frances H. Arnold,et al.  Exploring Nonnatural Evolutionary Pathways by Saturation Mutagenesis: Rapid Improvement of Protein Function , 1999, Journal of Molecular Evolution.

[3]  Nicolas E. Buchler,et al.  Universal correlation between energy gap and foldability for the random energy model and lattice proteins , 1999 .

[4]  P. Stadler,et al.  Viral RNA and evolved mutational robustness. , 1999, The Journal of experimental zoology.

[5]  R. Roberts,et al.  In vitro selection of nucleic acids and proteins: What are we learning? , 1999, Current opinion in structural biology.

[6]  F. Arnold,et al.  Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation , 1999, Nature.

[7]  M Kokkinidis,et al.  Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution. , 1999, Structure.

[8]  R. Sauer,et al.  Evolution of a protein fold in vitro. , 1999, Science.

[9]  C. Wilke,et al.  Adaptive walks on time-dependent fitness landscapes. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[10]  E. Shakhnovich,et al.  STABILITY OF DESIGNED PROTEINS AGAINST MUTATIONS , 1998, cond-mat/9809410.

[11]  Michael C. Flickinger,et al.  Encyclopedia of bioprocess technology : fermentation, biocatalysis, and bioseparation , 1999 .

[12]  F. Arnold,et al.  Directed evolution converts subtilisin E into a functional equivalent of thermitase. , 1999, Protein engineering.

[13]  Nicolas E. Buchler,et al.  Effect of alphabet size and foldability requirements on protein structure designability , 1999, Proteins.

[14]  P. Schuster,et al.  Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. , 1998, Journal of theoretical biology.

[15]  T. Yomo,et al.  Nonadditivity of mutational effects on the properties of catalase I and its application to efficient directed evolution. , 1998, Protein engineering.

[16]  G. Georgiou,et al.  Antibody affinity maturation using bacterial surface display. , 1998, Protein engineering.

[17]  T. Dewey,et al.  Non-equilibrium thermodynamics of molecular evolution. , 1998, Journal of theoretical biology.

[18]  Y. Husimi,et al.  Adaptive Walks by the Fittest among Finite Random Mutants on a Mt. Fuji-type Fitness Landscape. , 1998, Journal of theoretical biology.

[19]  P. Schuster,et al.  IR-98-039 / April Continuity in Evolution : On the Nature of Transitions , 1998 .

[20]  David C. Jones,et al.  Assessing the impact of secondary structure and solvent accessibility on protein evolution. , 1998, Genetics.

[21]  Y. Husimi,et al.  Fitness Landscape of a Biopolymer Participating in a Multi-step Reaction , 1998 .

[22]  B Levitan,et al.  Stochastic modeling and optimization of phage display. , 1998, Journal of molecular biology.

[23]  S. Bornholdt Genetic algorithm dynamics on a rugged landscape , 1998, cond-mat/9903076.

[24]  Frances H. Arnold,et al.  Molecular evolution by staggered extension process (StEP) in vitro recombination , 1998, Nature Biotechnology.

[25]  Fengzhu Sun,et al.  Modeling DNA shuffling , 1998, RECOMB '98.

[26]  D Bonnaz,et al.  Stochastic model of evolving populations , 1998 .

[27]  W. Stemmer,et al.  DNA shuffling of a family of genes from diverse species accelerates directed evolution , 1998, Nature.

[28]  E. Shakhnovich,et al.  Folding and misfolding of designed proteinlike chains with mutations , 1998 .

[29]  F. Arnold,et al.  Random-priming in vitro recombination: an effective tool for directed evolution. , 1998, Nucleic acids research.

[30]  F. Arnold,et al.  Directed evolution of enzyme catalysts. , 1997, Trends in biotechnology.

[31]  L. Loeb,et al.  Creating novel enzymes by applied molecular evolution. , 1997, Chemistry & biology.

[32]  R A Goldstein,et al.  Evolution of model proteins on a foldability landscape , 1997, Proteins.

[33]  E. Bornberg-Bauer,et al.  How are model protein structures distributed in sequence space? , 1997, Biophysical journal.

[34]  R A Goldstein,et al.  The foldability landscape of model proteins , 1997, Biopolymers.

[35]  S. L. Mayo,et al.  De novo protein design: fully automated sequence selection. , 1997, Science.

[36]  Jeffery G. Saven,et al.  STATISTICAL MECHANICS OF THE COMBINATORIAL SYNTHESIS AND ANALYSIS OF FOLDING MACROMOLECULES , 1997 .

[37]  P. Stadler,et al.  Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. , 1997, Folding & design.

[38]  F. Arnold,et al.  Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. , 1997, Journal of molecular biology.

[39]  Inman Harvey,et al.  Fourth European Conference on Artificial Life , 1997 .

[40]  Peter F. Stadler,et al.  Correlation length, isotropy and meta-stable states , 1997 .

[41]  F. Arnold,et al.  Combinatorial protein design: strategies for screening protein libraries. , 1997, Current opinion in structural biology.

[42]  A. Prügel-Bennett,et al.  The dynamics of a genetic algorithm for simple random Ising systems , 1997 .

[43]  Yi-Cheng Zhang QUASISPECIES EVOLUTION OF FINITE POPULATIONS , 1997 .

[44]  F. Arnold,et al.  Optimization of DNA shuffling for high fidelity recombination. , 1997, Nucleic acids research.

[45]  P. Schuster,et al.  Generic properties of combinatory maps: neutral networks of RNA secondary structures. , 1997, Bulletin of mathematical biology.

[46]  W. H. Moos,et al.  Annual Reports in Combinatorial Chemistry and Molecular Diversity , 1997, Annual Reports in Combinatorial Chemistry and Molecular Diversity.

[47]  Y Husimi,et al.  Fitness spectrum among random mutants on Mt. Fuji-type fitness landscape. , 1996, Journal of theoretical biology.

[48]  N. Wingreen,et al.  Emergence of Preferred Structures in a Simple Model of Protein Folding , 1996, Science.

[49]  F. Arnold,et al.  Engineering new functions and altering existing functions. , 1996, Current opinion in structural biology.

[50]  T G Dewey,et al.  The Shannon information entropy of protein sequences. , 1996, Biophysical journal.

[51]  Wolynes,et al.  Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding. , 1996, Physical review letters.

[52]  A. Wagner DOES EVOLUTIONARY PLASTICITY EVOLVE? , 1996, Evolution; international journal of organic evolution.

[53]  A Godzik,et al.  Structural diversity in a family of homologous proteins. , 1996, Journal of molecular biology.

[54]  David T. Jones,et al.  Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin‐43, an α‐helical protein with over 50% sequence identity to an all‐β protein , 1996 .

[55]  P Koehl,et al.  Mean-field minimization methods for biological macromolecules. , 1996, Current opinion in structural biology.

[56]  Frances H. Arnold,et al.  Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents , 1996, Nature Biotechnology.

[57]  P. Stadler Landscapes and their correlation functions , 1996 .

[58]  F. Arnold,et al.  Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. , 1996, Protein engineering.

[59]  Melanie Mitchell,et al.  An introduction to genetic algorithms , 1996 .

[60]  Y C Chen,et al.  A mathematical model for biopanning (affinity selection) using peptide libraries on filamentous phage. , 1995, Journal of theoretical biology.

[61]  B K Shoichet,et al.  Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. , 1995, Protein engineering.

[62]  E I Shakhnovich,et al.  Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. , 1995, Journal of molecular biology.

[63]  Bernard Manderick,et al.  The Usefulness of Recombination , 1995, ECAL.

[64]  A. E. Eiben,et al.  Orgy in the Computer: Multi-Parent Reproduction in Genetic Algorithms , 1995, ECAL.

[65]  S. Kauffman,et al.  Search strategies for applied molecular evolution. , 1995, Journal of theoretical biology.

[66]  D. Yee,et al.  Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.

[67]  G. K. Ackers,et al.  Long-range, small magnitude nonadditivity of mutational effects in proteins. , 1995, Biochemistry.

[68]  E. Goldman,et al.  Context dependence of phenotype prediction and diversity in combinatorial mutagenesis. , 1995, Protein engineering.

[69]  T. Yomo,et al.  Experimental sketch of landscapes in protein sequence space , 1995 .

[70]  W. Hendrickson,et al.  Quantification of tertiary structural conservation despite primary sequence drift in the globin fold , 1994, Protein science : a publication of the Protein Society.

[71]  Peter F. Stadler,et al.  Landscapes: Complex Optimization Problems and Biopolymer Structures , 1994, Comput. Chem..

[72]  W. Stemmer Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[73]  E. Shakhnovich,et al.  Proteins with selected sequences fold into unique native conformation. , 1994, Physical review letters.

[74]  A. Clarke,et al.  Engineering surface loops of proteins--a preferred strategy for obtaining new enzyme function. , 1994, Trends in biotechnology.

[75]  Roland L. Dunbrack,et al.  Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains , 1994, Nature Structural Biology.

[76]  Prügel-Bennett,et al.  Analysis of genetic algorithms using statistical mechanics. , 1994, Physical review letters.

[77]  C. Lee,et al.  Predicting protein mutant energetics by self-consistent ensemble optimization. , 1994, Journal of molecular biology.

[78]  L. Booker Foundations of genetic algorithms. 2: L. Darrell Whitley (Ed.), Morgan Kaufmann, San Mateo, CA, 1993, ISBN 1-55860-263-1, 322 pp., US$45.95 , 1994 .

[79]  Larry J. Eshelman,et al.  Productive Recombination and Propagating and Preserving Schemata , 1994, FOGA.

[80]  John J. Grefenstette Predictive Models Using Fitness Distributions of Genetic Operators , 1994, FOGA.

[81]  M. Black,et al.  Selection of new biologically active molecules from random nucleotide sequences. , 1993, Gene.

[82]  P. Stadler,et al.  Anisotropy in fitness landscapes. , 1993, Journal of theoretical biology.

[83]  D. Youvan,et al.  Searching Sequence Space to Engineer Proteins: Exponential Ensemble Mutagenesis , 1993, Bio/Technology.

[84]  Peter F. Stadler,et al.  Error Thresholds on Correlated Fitness Landscapes , 1993 .

[85]  S Forrest,et al.  Genetic algorithms , 1996, CSUR.

[86]  Jean-Marie Dubois,et al.  Darwinian Adaptative Simulated Annealing , 1993 .

[87]  Weinberger,et al.  RNA folding and combinatory landscapes. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[88]  Asparate transcarbamoylase: Current opinion in structural biology 1993, 3:960–967 , 1993 .

[89]  F M Richards,et al.  The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions. , 1992, Biochemistry.

[90]  Peter F. Stadler,et al.  Correlation in Landscapes of Combinatorial Optimization Problems , 1992 .

[91]  Flyvbjerg,et al.  Coevolution in a rugged fitness landscape. , 1992, Physical review. A, Atomic, molecular, and optical physics.

[92]  S. Kauffman,et al.  Applied molecular evolution. , 1992, Journal of theoretical biology.

[93]  M. Feldman,et al.  Recombination dynamics and the fitness landscape , 1992 .

[94]  William M. Spears,et al.  Crossover or Mutation? , 1992, FOGA.

[95]  Melanie Mitchell,et al.  Relative Building-Block Fitness and the Building Block Hypothesis , 1992, FOGA.

[96]  P. Wolynes,et al.  The energy landscapes and motions of proteins. , 1991, Science.

[97]  C. Tuerk,et al.  SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. , 1991, Journal of molecular biology.

[98]  Weinberger,et al.  Local properties of Kauffman's N-k model: A tunably rugged energy landscape. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[99]  R. Houghten,et al.  Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery , 1991, Nature.

[100]  P. Holmes,et al.  1989 Lectures in Complex Systems , 1991 .

[101]  M. Kimura The neutral theory of molecular evolution: a review of recent evidence. , 1991, Idengaku zasshi.

[102]  Lashon B. Booker,et al.  Proceedings of the fourth international conference on Genetic algorithms , 1991 .

[103]  A. Perelson,et al.  Evolutionary walks on rugged landscapes , 1991 .

[104]  H. Tachida A study on a nearly neutral mutation model in finite populations. , 1991, Genetics.

[105]  J. Knowles,et al.  Enzyme catalysis: not different, just better , 1991, Nature.

[106]  R. Lerner,et al.  The enzymic nature of antibody catalysis: development of multistep kinetic processing. , 1990, Science.

[107]  A. Houston,et al.  Genetic algorithms and evolution. , 1990, Journal of theoretical biology.

[108]  Wen-Hsiung Li,et al.  Fundamentals of molecular evolution , 1990 .

[109]  J. Wells,et al.  Additivity of mutational effects in proteins. , 1990, Biochemistry.

[110]  G. Wagner,et al.  QUANTITATIVE VARIATION IN FINITE PARTHENOGENETIC POPULATIONS: WHAT STOPS MULLER'S RATCHET IN THE ABSENCE OF RECOMBINATION? , 1990, Evolution; international journal of organic evolution.

[111]  Robert T. Sauer,et al.  Functionally acceptable substitutions in two α‐helical regions of λ repressor , 1990, Proteins.

[112]  Larry J. Eshelman,et al.  Spurious Correlations and Premature Convergence in Genetic Algorithms , 1990, FOGA.

[113]  J. David Schaffer,et al.  Proceedings of the third international conference on Genetic algorithms , 1989 .

[114]  E. D. Weinberger,et al.  The NK model of rugged fitness landscapes and its application to maturation of the immune response. , 1989, Journal of theoretical biology.

[115]  Schuster,et al.  Physical aspects of evolutionary optimization and adaptation. , 1989, Physical review. A, General physics.

[116]  M. Nowak,et al.  Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet. , 1989, Journal of theoretical biology.

[117]  M. Eigen,et al.  Molecular quasi-species. , 1988 .

[118]  R. Sauer,et al.  Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. , 1988, Science.

[119]  J. Gerlt,et al.  Identification of residues involved in a conformational change accompanying substitutions for glutamate-43 in staphylococcal nuclease. , 1988, Biochemistry.

[120]  H. M. Geysen,et al.  Strategies for epitope analysis using peptide synthesis. , 1987, Journal of immunological methods.

[121]  S. Kauffman,et al.  Towards a general theory of adaptive walks on rugged landscapes. , 1987, Journal of theoretical biology.

[122]  P. Schuster,et al.  A computer model of evolutionary optimization. , 1987, Biophysical chemistry.

[123]  G. L. Hofacker,et al.  Point mutations as an optimal search process in biological evolution. , 1987, Journal of theoretical biology.

[124]  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.

[125]  John Maynard Smith,et al.  When learning guides evolution , 1987, Nature.

[126]  P G Schultz,et al.  Selective chemical catalysis by an antibody. , 1986, Science.

[127]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[128]  R. Brady Optimization strategies gleaned from biological evolution , 1985, Nature.

[129]  R. Jernigan,et al.  Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .

[130]  J. Gillespie MOLECULAR EVOLUTION OVER THE MUTATIONAL LANDSCAPE , 1984, Evolution; international journal of organic evolution.

[131]  H. M. Martinez,et al.  An RNA folding rule , 1984, Nucleic Acids Res..

[132]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[133]  B. Derrida Random-energy model: An exactly solvable model of disordered systems , 1981 .

[134]  B. Derrida Random-Energy Model: Limit of a Family of Disordered Models , 1980 .

[135]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[136]  G. Oster,et al.  Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination. , 1979, Journal of theoretical biology.

[137]  S. Kirkpatrick,et al.  Solvable Model of a Spin-Glass , 1975 .

[138]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[139]  T. Ohta Slightly Deleterious Mutant Substitutions in Evolution , 1973, Nature.

[140]  G. Lienhard,et al.  Enzymatic Catalysis and Transition-State Theory , 1973, Science.

[141]  John Maynard Smith,et al.  Natural Selection and the Concept of a Protein Space , 1970, Nature.

[142]  J. L. King,et al.  Non-Darwinian evolution. , 1969, Science.

[143]  H. Muller THE RELATION OF RECOMBINATION TO MUTATIONAL ADVANCE. , 1964, Mutation research.

[144]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[145]  Richard W. Hamming,et al.  Error detecting and error correcting codes , 1950 .