Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles
暂无分享,去创建一个
Vijay S Pande | Stefan M. Larson | Jeremy L. England | Stefan M Larson | Jeremy L England | John R Desjarlais | V. Pande | S. Larson | J. Desjarlais
[1] 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.
[2] D. Baker,et al. Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.
[3] S. Bryant,et al. Threading a database of protein cores , 1995, Proteins.
[4] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .
[5] N. Wingreen,et al. The designability of protein structures. , 2001, Journal of molecular graphics & modelling.
[6] Andrea Musacchio,et al. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides , 1994, Nature Structural Biology.
[7] M. Levitt,et al. De novo protein design. I. In search of stability and specificity. , 1999, Journal of molecular biology.
[8] C. Gustafsson,et al. Directed evolution: the 'rational' basis for 'irrational' design. , 2000, Current opinion in structural biology.
[9] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[10] Andrew M Wollacott,et al. Prediction of amino acid sequence from structure , 2000, Protein science : a publication of the Protein Society.
[11] N. Wingreen,et al. Emergence of Preferred Structures in a Simple Model of Protein Folding , 1996, Science.
[12] C. Chothia. Proteins. One thousand families for the molecular biologist. , 1992, Nature.
[13] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[14] B. Dahiyat,et al. In silico design for protein stabilization. , 1999, Current opinion in biotechnology.
[15] H Kono,et al. Statistical Theory for Protein Combinatorial Libraries , 2001 .
[16] E I Shakhnovich,et al. Protein design: a perspective from simple tractable models , 1998, Folding & design.
[17] Nicolas E. Buchler,et al. Effect of alphabet size and foldability requirements on protein structure designability , 1999, Proteins.
[18] Christopher A. Voigt,et al. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. , 2000, Journal of molecular biology.
[19] D. Baker,et al. Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[20] Yanli Wang,et al. MMDB: 3D structure data in Entrez , 2000, Nucleic Acids Res..
[21] David T. Jones,et al. Protein superfamilles and domain superfolds , 1994, Nature.
[22] B. Matthews,et al. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. , 1992, Science.
[23] Patrice Koehl,et al. Protein topology and stability define the space of allowed sequences , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[24] S. Henikoff,et al. Protein family classification based on searching a database of blocks. , 1994, Genomics.
[25] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[26] T M Handel,et al. Review: protein design--where we were, where we are, where we're going. , 2001, Journal of structural biology.
[27] R. Kazlauskas,et al. Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. , 2000, Current opinion in chemical biology.
[28] B. Erman,et al. Information‐theoretical entropy as a measure of sequence variability , 1991, Proteins.
[29] S J Wodak,et al. Automatic protein design with all atom force-fields by exact and heuristic optimization. , 2000, Journal of molecular biology.
[30] Michael R. Shirts,et al. COMPUTING: Screen Savers of the World Unite! , 2000, Science.
[31] Stephen L. Mayo,et al. Design, structure and stability of a hyperthermophilic protein variant , 1998, Nature Structural Biology.
[32] J G Saven,et al. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. , 2001, Journal of molecular biology.
[33] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[34] A. Ménez,et al. Tailoring new enzyme functions by rational redesign. , 2000, Current opinion in structural biology.
[35] P. S. Kim,et al. High-resolution protein design with backbone freedom. , 1998, Science.
[36] P. Koehl,et al. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. , 1994, Journal of molecular biology.
[37] N S Wingreen,et al. Are protein folds atypical? , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[38] J G Saven,et al. Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. , 2000, Journal of molecular biology.
[39] C. Lee,et al. Predicting protein mutant energetics by self-consistent ensemble optimization. , 1994, Journal of molecular biology.
[40] S L Mayo,et al. Coupling backbone flexibility and amino acid sequence selection in protein design , 1997, Protein science : a publication of the Protein Society.
[41] M. Levitt,et al. Improved recognition of native-like protein structures using a family of designed sequences , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[42] C. Chothia. One thousand families for the molecular biologist , 1992, Nature.
[43] Stefan M. Larson,et al. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. , 2000, Journal of molecular biology.
[44] J R Desjarlais,et al. Computer search algorithms in protein modification and design. , 1998, Current opinion in structural biology.
[45] Vijay S. Pande,et al. Screen Savers of the World Unite! , 2000, Science.
[46] J R Desjarlais,et al. Side-chain and backbone flexibility in protein core design. , 1999, Journal of molecular biology.
[47] B. Matthews,et al. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. , 1994, Science.
[48] M. Levitt,et al. De novo protein design. II. Plasticity in sequence space. , 1999, Journal of molecular biology.
[49] Chen Zeng,et al. Emergence of highly designable protein‐backbone conformations in an off‐lattice model , 2001, Proteins.
[50] C. Chothia,et al. Population statistics of protein structures: lessons from structural classifications. , 1997, Current opinion in structural biology.
[51] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[52] V S Pande,et al. Statistical mechanics of simple models of protein folding and design. , 1997, Biophysical journal.
[53] U. Bornscheuer,et al. Improved biocatalysts by directed evolution and rational protein design. , 2001, Current opinion in chemical biology.
[54] J R Desjarlais,et al. De novo design of the hydrophobic cores of proteins , 1995, Protein science : a publication of the Protein Society.
[55] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[56] C. Pabo. Molecular technology: Designing proteins and peptides , 1983, Nature.