De novo protein design using pairwise potentials and a genetic algorithm

No abstract is available for this paper.

• Publication year

  1994

• Venue

  Protein Science

• Publication date

  1994-04-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1002/PRO.5560030405PMID 8003975PMCID PMC2142856
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Genetic algorithms and their applications

  1996influential reference
• Protein fold recognition

  1993cited by this paper
• Three-dimensional structure of acylphosphatase. Refinement and structure analysis.

  1992cited by this paper
• Contact potential that recognizes the correct folding of globular proteins.

  1992cited by this paper
• A new approach to protein fold recognition

  1992cited by this paper
• Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida

  1992cited by this paper
• Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.

  1992cited by this paper
• Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations

  1992cited by this paper
• The SWISS-PROT protein sequence data bank.

  1991cited by this paper
• A method to identify protein sequences that fold into a known three-dimensional structure.

  1991cited by this paper
• A new approach to the rapid determination of protein side chain conformations.

  1991cited by this paper
• A program to produce both detailed and schematic plots of protein structures

  1991cited by this paper
• Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.

  1990cited by this paper
• De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.

  1990cited by this paper
• Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

  1990cited by this paper
• A fast algorithm for rendering space-filling molecule pictures

  1988cited by this paper
• Characterization of a helical protein designed from first principles.

  1988cited by this paper
• Genetic Algorithms in Search Optimization and Machine Learning

  1988cited by this paper
• Reducing Bias and Inefficienry in the Selection Algorithm

  1987cited by this paper
• The folding type of a protein is relevant to the amino acid composition.

  1986cited by this paper
• Radial locations of amino acid residues in a globular protein: correlation with the sequence.

  1986cited by this paper
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983influential reference
• Molecular engineering: An approach to the development of general capabilities for molecular manipulation.

  1981cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• New Approach.

  1953cited by this paper

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  2021cites this paper
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  2020cites this paper
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  2019cites this paper
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  2019cites this paper
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  2018cites this paper
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  2018cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2016cites this paper
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  2016cites this paper
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  2016cites this paper
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  2015cites this paper
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  2015cites this paper
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  2015cites this paper
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  2014cites this paper
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  2014cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2012cites this paper
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  2012cites this paper
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  2012cites this paper
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  2012cites this paper
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  2011cites this paper
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  2011cites this paper
• Kay, Lewis E.: Structure and Dynamics of Proteins – Big and Small

  2010cites this paper
• Peptides as Molecular Receptors

  2010cites this paper
• Combinatorial design of protein sequences with applications to lattice and real proteins.

  2009cites this paper
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  2009cites this paper
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  2009cites this paper
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  2009cites this paper
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  2009cites this paper
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  2009cites this paper
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  2009cites this paper
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  2008cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2006cites this paper
• Computational protein design: a novel path to future protein drugs.

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  2005cites this paper
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  2005cites this paper
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  2005cites this paper
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  2005cites this paper
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  2004cites this paper
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  2004cites this paper
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  2004cites this paper
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  2004cites this paper
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  2003cites this paper
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  2003cites this paper
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  2003cites this paper
• Computationally optimizing the directed evolution of proteins

  2003cites this paper
• Genetic and Evolutionary Algorithms

  2002cites this paper
• Combinatorial protein design.

  2002cites this paper
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  2002cites this paper
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  2002cites this paper
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  2002cites this paper
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  2001cites this paper
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  2001cites this paper
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  2001cites this paper