Evolutionary Algorithms for the Inverse Protein Folding Problem

[1]  Pascal Bouvry,et al.  Management of an academic HPC cluster: The UL experience , 2014, 2014 International Conference on High Performance Computing & Simulation (HPCS).

[2]  Pascal Bouvry,et al.  Cooperative Selection: Improving Tournament Selection via Altruism , 2014, EvoCOP.

[3]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[4]  Yang Zhang,et al.  An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis , 2013, PLoS Comput. Biol..

[5]  Florian Klein,et al.  Antibodies in HIV-1 Vaccine Development and Therapy , 2013, Science.

[6]  Christodoulos A Floudas,et al.  Protein WISDOM: a workbench for in silico de novo design of biomolecules. , 2013, Journal of visualized experiments : JoVE.

[7]  Günter Rudolph,et al.  Niching by multiobjectivization with neighbor information: Trade-offs and benefits , 2013, 2013 IEEE Congress on Evolutionary Computation.

[8]  H. K. Fung,et al.  Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework. , 2010, Biophysical journal.

[9]  Kalyanmoy Deb,et al.  Finding multiple solutions for multimodal optimization problems using a multi-objective evolutionary approach , 2010, GECCO '10.

[10]  H. K. Fung,et al.  New compstatin variants through two de novo protein design frameworks. , 2010, Biophysical journal.

[11]  Yang Zhang,et al.  How significant is a protein structure similarity with TM-score = 0.5? , 2010, Bioinform..

[12]  Martin S. Taylor,et al.  Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. , 2008, Biophysical journal.

[13]  Enrique Alba,et al.  The exploration/exploitation tradeoff in dynamic cellular genetic algorithms , 2005, IEEE Transactions on Evolutionary Computation.

[14]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[15]  John L. Klepeis,et al.  Design of peptide analogues with improved activity using a novel de novo protein design approach , 2004 .

[16]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[17]  Ernesto Benini,et al.  Genetic Diversity as an Objective in Multi-Objective Evolutionary Algorithms , 2003, Evolutionary Computation.

[18]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[19]  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.

[20]  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.

[21]  S J Wodak,et al.  Automatic protein design with all atom force-fields by exact and heuristic optimization. , 2000, Journal of molecular biology.

[22]  K Nishikawa,et al.  Design and synthesis of a globin fold. , 1999, Biochemistry.

[23]  A Mulchandani,et al.  Engineering of improved microbes and enzymes for bioremediation. , 1999, Current opinion in biotechnology.

[24]  P. S. Kim,et al.  High-resolution protein design with backbone freedom. , 1998, Science.

[25]  Hisashi Shimodaira,et al.  DCGA: a diversity control oriented genetic algorithm , 1997, Proceedings Ninth IEEE International Conference on Tools with Artificial Intelligence.

[26]  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.

[27]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[28]  David T. Jones,et al.  De novo protein design using pairwise potentials and a genetic algorithm , 1994, Protein science : a publication of the Protein Society.

[29]  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.

[30]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[31]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[32]  C. Pabo.  Molecular technology: Designing proteins and peptides , 1983, Nature.

[33]  Drexler Ke,et al.  Molecular engineering: An approach to the development of general capabilities for molecular manipulation. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[34]  B. Gutte,et al.  Design, synthesis and characterisation of a 34-residue polypeptide that interacts with nucleic acids , 1979, Nature.

[35]  Kenneth Alan De Jong,et al.  An analysis of the behavior of a class of genetic adaptive systems. , 1975 .

[36]  F. Wilcoxon.  Individual Comparisons by Ranking Methods , 1945 .