PDB-based protein loop prediction: parameters for selection and methods for optimization.

No abstract is available for this paper.

• Publication year

  1997

• Venue

  Journal of Molecular Biology

• Publication date

  1997-04-11

• Fields of study

  Biology, Medicine, Physics, Computer Science

• Identifiers
  DOI 10.1006/JMBI.1996.0857PMID 9135125
• 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.

• Sidechain and backbone potential function for conformational analysis of proteins.

  2009cited by this paper
• Comparison of an antibody model with an X‐ray structure: The variable fragment of BR96

  1996cited by this paper
• Accuracy and reliability of the scaling‐relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational samplings

  1996cited by this paper
• Modeling mutations and homologous proteins.

  1995cited by this paper
• Prediction of hypervariable CDR-H3 loop structures in antibodies.

  1995cited by this paper
• A critical assessment of comparative molecular modeling of tertiary structures of proteins *

  1995cited by this paper
• Simultaneous modeling of multiple loops in proteins

  1995cited by this paper
• Comparison of systematic search and database methods for constructing segments of protein structure.

  1994influential reference
• Analysis of two-residue turns in proteins.

  1994cited by this paper
• A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603.

  1994cited by this paper
• Evaluation of the conformational free energies of loops in proteins

  1994cited by this paper
• Design, creation, and characterization of a stable, monomeric triosephosphate isomerase.

  1994cited by this paper
• Conformational Sampling of Loop Structures Using Genetic Algorithms

  1994cited by this paper
• Protein superfamilles and domain superfolds

  1994cited by this paper
• Derivation of rules for comparative protein modeling from a database of protein structure alignments

  1994cited by this paper
• Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations

  1994cited by this paper
• The loop problem in proteins: A monte carlo simulated annealing approach

  1993influential reference
• Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant.

  1993cited by this paper
• Conformation of complementarity determining region L1 loop in murine IgG lambda light chain extends the repertoire of canonical forms.

  1993cited by this paper
• A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

  1993cited by this paper
• Analysis of the genetic algorithm method of molecular conformation determination

  1993cited by this paper
• Loop closure via bond scaling and relaxation

  1993cited by this paper
• Modeling of protein loops by simulated annealing

  1993cited by this paper
• Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms

  1993cited by this paper
• Determining protein loop conformation using scaling‐relaxation techniques

  1993cited by this paper
• A method for predicting protein structure from sequence.

  1993cited by this paper
• Backbone-dependent rotamer library for proteins. Application to side-chain prediction.

  1993cited by this paper
• Anti‐insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent

  1992influential reference
• Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides

  1992cited by this paper
• Common features of the conformations of antigen‐binding loops in immunoglobulins and application to modeling loop conformations

  1992influential reference
• Amino acid substitution matrices from protein blocks.

  1992cited by this paper
• Exhaustive matching of the entire protein sequence database.

  1992cited by this paper
• A data bank merging related protein structures and sequences.

  1992cited by this paper
• Taxonomy and conformational analysis of loops in proteins.

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• Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

  1992cited by this paper
• Structural repertoire of the human VH segments.

  1992influential reference
• Search for the stable state of a short chain in a molecular field.

  1992cited by this paper
• Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units

  1992cited by this paper
• Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles.

  1991cited by this paper
• Determining minimum energy conformations of polypeptides by dynamic programming

  1990cited by this paper
• Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops

  1990cited by this paper
• Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

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• Conformational sampling using high‐temperature molecular dynamics

  1990cited by this paper
• Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.

  1990cited by this paper
• Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations.

  1990influential reference
• Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.

  1989cited by this paper
• Conformations of immunoglobulin hypervariable regions

  1989influential reference
• Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease.

  1989cited by this paper
• Modelling the polypeptide backbone with 'spare parts' from known protein structures.

  1989cited by this paper
• Modeling antibody hypervariable loops: a combined algorithm.

  1989cited by this paper
• Protein folding

  1988cited by this paper
• Structure of antibody hypervariable loops reproduced by a conformational search algorithm

  1988cited by this paper
• Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix.

  1988cited by this paper
• Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures

  1987cited by this paper
• Canonical structures for the hypervariable regions of immunoglobulins.

  1987influential reference
• An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

  1986cited by this paper
• Using known substructures in protein model building and crystallography.

  1986influential reference
• Loops in globular proteins: a novel category of secondary structure.

  1986influential reference
• Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

  1986cited by this paper
• Chain closure with bond angle variations

  1985cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983influential reference
• Model for haptoglobin heavy chain based upon structural homology.

  1980cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• A solution for the best rotation to relate two sets of vectors

  1976cited by this paper
• A simplified representation of protein conformations for rapid simulation of protein folding.

  1976influential reference
• \the Protein Data Bank: a Computer-based Archival Le for Macromolecular Structures,"

  year unknowninfluential reference

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• Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent

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• Template-based protein structure modeling.

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• Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

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• The function of the extracellular regions in opioid receptor binding: insights from computational biology.

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