On Potential Energy Models for EA-based Ab Initio Protein Structure Prediction

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Evolutionary Computation

• Publication date

  2010-06-01

• Fields of study

  Biology, Physics, Chemistry, Computer Science, Medicine

• Identifiers
  DOI 10.1162/evco.2010.18.2.18204PMID 20210597
• 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.

• Protein data bank

  2012influential reference
• Towards in Silico Rational De Novo Design of Peptides for Inorganic Interfaces

  2008cited by this paper
• Study of conformational switching in polyalanine at solid surfaces using molecular simulation

  2007cited by this paper
• DIMACS Series in Discrete Mathematicsand Theoretical Computer Science Global Optimization Approaches in Protein Folding andPeptide

  2007cited by this paper
• Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance

  2006influential reference
• Ab initio protein fold prediction using evolutionary algorithms

  2006influential reference
• Chapter 7 Empirical Force Fields for Proteins: Current Status and Future Directions

  2005cited by this paper
• The interaction of proteins with solid surfaces.

  2004influential reference
• Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

  2004cited by this paper
• Energy Landscape of Met-Enkephalin and Leu-Enkephalin Drawn Using Mutually Orthogonal Latin Squares Sampling

  2004cited by this paper
• A multidimensional 1H NMR investigation of the conformation of methionine-enkephalin in fast-tumbling bicelles.

  2004cited by this paper
• A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

  2003cited by this paper
• Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

  2003cited by this paper
• Force fields for protein simulations.

  2003cited by this paper
• An overview of Genetic Algorithms

  2003cited by this paper
• Function first: a powerful approach to post-genomic drug discovery.

  2002influential reference
• Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models.

  2002cited by this paper
• Nature's Complex Copolymers: Engineering Design of Oligopeptide Materials

  2002cited by this paper
• α-Helical stabilization by side chain shielding of backbone hydrogen bonds

  2002cited by this paper
• A genetic algorithm for shortest path routing problem and the sizing of populations

  2002cited by this paper
• Progress in the analysis of membrane protein structure and function

  2002cited by this paper
• Rotamer libraries in the 21st century.

  2002cited by this paper
• Recent developments in computational proteomics.

  2001influential reference
• Protein Structure Prediction and Structural Genomics

  2001cited by this paper
• Recent developments in computational proteomics.

  2001cited by this paper
• Natural peptide analgesics: the role of solution conformation

  2001cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Ab initio protein folding.

  2000cited by this paper
• Modelling the Dynamics of a Steady State Genetic Algorithm

  1999cited by this paper
• Free energy calculations for peptides via deterministic global optimization

  1999cited by this paper
• New Monte Carlo algorithms for protein folding.

  1999cited by this paper
• Functionalization and Properties of Designed Folded Polypeptides

  1999cited by this paper
• Protein dynamics simulations from nanoseconds to microseconds.

  1999cited by this paper
• Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0

  1999influential reference
• Biological surface science

  1998influential reference
• New optimization method for conformational energy calculations on polypeptides: Conformational space annealing

  1997influential reference
• Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure

  1997cited by this paper
• Prediction of Oligopeptide Conformations via Deterministic Global Optimization

  1997cited by this paper
• Can drugs be designed?

  1997cited by this paper
• Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics

  1997cited by this paper
• A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

  1996influential reference
• Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

  1996influential reference
• The Density of States - A Measure of the Difficulty of Optimisation Problems

  1996influential reference
• Genetic Algorithms + Data Structures = Evolution Programs

  1996cited by this paper
• Genetic algorithms + data structures = evolution programs (3rd ed.)

  1996cited by this paper
• Fitness Distance Correlation as a Measure of Problem Difficulty for Genetic Algorithms

  1995influential reference
• On genetic algorithms

  1995cited by this paper
• Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides

  1994influential reference
• Fitness landscapes and difficulty in genetic programming

  1994cited by this paper
• Knowledge-based protein modeling.

  1994cited by this paper
• The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins

  1994influential reference
• Genetic Algorithms for Protein Tertiary Structure Prediction

  1993cited by this paper
• An Overview of Genetic Algorithms: Part 2, Research Topics

  1993cited by this paper
• The application of the genetic algorithm to the minimization of potential energy functions

  1993influential reference
• Numerical recipes in C (2nd ed.): the art of scientific computing

  1992cited by this paper
• Conformational study of met-enkephalin in its zwitterionic form

  1992cited by this paper
• Genetic Operators, the Fitness Landscape and the Traveling Salesman Problem

  1992influential reference
• Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence

  1992cited by this paper
• An Overview of Genetic Algorithms

  1992cited by this paper
• Numerical Recipes in C, 2nd Edition

  1992cited by this paper
• Mean field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and met-enkephalin

  1992cited by this paper
• A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin

  1991cited by this paper
• Extended Selection Mechanisms in Genetic Algorithms

  1991cited by this paper
• Representational issues in genetic optimization

  1990influential reference
• A Study of Reproduction in Generational and Steady State Genetic Algorithms

  1990influential reference
• Handbook Of Genetic Algorithms

  1990cited by this paper
• A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method.

  1989cited by this paper
• The multiple-minima problem in the conformational analysis of polypeptides. III. An Electrostatically Driven Monte Carlo Method: Tests on enkephalin

  1989cited by this paper
• Molecular-dynamics simulations of [Met5]- and [D-Ala2,Met5]-enkephalins. Biological implication of monomeric folded and dimeric unfolded conformations.

  1988cited by this paper
• Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system

  1988influential reference
• An all atom force field for simulations of proteins and nucleic acids

  1986cited by this paper
• Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations

  1984influential reference
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983influential reference
• Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

  1983cited by this paper
• Met-enkephalin and related peptides in man.

  1982cited by this paper
• Genetic algorithms for function optimization

  1980cited by this paper
• An Analysis Of The Behavior Of A Class Of Genetic Adaptive Systems

  1975cited by this paper
• Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids

  1975cited by this paper
• Molecular Structure of N-Methylformamide as Studied by Gas Electron Diffraction

  1973cited by this paper
• The Nature of the Chemical Bond and the Structure of Molecules and Crystals: An Introduction to Modern Structural Chemistry.

  1960cited by this paper
• The nature of the chemical bond and the structure of molecules and crystals : an introduction to modern structural chemistry.

  1960cited by this paper
• The Molecular Structure of N-Methylacetamide

  1950cited by this paper

• Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures

  2023cites this paper
• ADEMO/D: An adaptive differential evolution for protein structure prediction problem

  2016cites this paper
• Predição da Estrutura de Proteínas Utilizando Algoritmo Evolutivo Adaptativo

  2015cites this paper
• A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

  2013cites this paper
• A Multiobjective Algorithm for Protein Structure Prediction Using Adaptive Differential Evolution

  2013cites this paper
• Evolving local minima in the protein energy surface

  2013cites this paper
• A population-based evolutionary algorithm for sampling minima in the protein energy surface

  2012cites this paper
• Local Minima Hopping along the Protein Energy Surface

  2012cites this paper
• Free energy of adsorption of proteins at fluid/solid interfaces using molecular simulation

  2011cites this paper