Does conformational free energy distinguish loop conformations in proteins? (Q42929125)

11 November 2017

Does conformational free energy distinguish loop conformations in proteins? (English)

1 reference

11 November 2017

1

1 reference

11 November 2017

Chen SW

2

1 reference

PMCID

1181139

11 November 2017

language of work or name

English

0 references

publication date

1 November 1997

1 reference

11 November 2017

17

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

11 November 2017

73

1 reference

11 November 2017

5

1 reference

11 November 2017

2359-2375

1 reference

Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex

11 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

On the prediction of protein structure: The significance of the root-mean-square deviation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

A comprehensive set of sequence analysis programs for the VAX

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Comparison of super-secondary structures in proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

The relation between the divergence of sequence and structure in proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Using known substructures in protein model building and crystallography

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Structure of antibody hypervariable loops reproduced by a conformational search algorithm

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Helix signals in proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Modeling antibody hypervariable loops: a combined algorithm.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Three-dimensional structure of an antibody-antigen complex

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Prediction of protein side-chain conformation by packing optimization.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

A new approach to the rapid determination of protein side chain conformations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Taxonomy and conformational analysis of loops in proteins.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Structural evidence for induced fit as a mechanism for antibody-antigen recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-Å resolution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

The Protein Data Bank: a computer-based archival file for macromolecular structures

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Evaluation of the conformational free energies of loops in proteins.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

The loop problem in proteins: a Monte Carlo simulated annealing approach.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181139

Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody

1 December 2018

1 reference

12 December 2020

A method to configure protein side-chains from the main-chain trace in homology modelling

1 reference

12 December 2020

Crystal Structure of the Complex of the Variable Domain of Antibody D1.3 and Turkey Egg White Lysozyme: A Novel Conformational Change in Antibody CDR-L3 Selects for Antigen

1 reference

12 December 2020

Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 A resolution

1 reference

12 December 2020

Prediction of the folding of short polypeptide segments by uniform conformational sampling

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

12 December 2020

Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures

1 reference

12 December 2020

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

12 December 2020

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

1 reference

12 December 2020

Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding

1 reference

12 December 2020

Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution

1 reference

12 December 2020

A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex

1 reference

12 December 2020

A systematic approach to the comparison of protein structures

1 reference

12 December 2020

Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 A and 1.0 A resolution

1 reference

12 December 2020

A hypothetical space-filling model of the V-regions of the galactan-binding myeloma immunoglobulin J539☆

1 reference

12 December 2020

A refined model for the variable domains (Fv) of the J539 beta(1,6)-D-galactan-binding immunoglobulin

1 reference

12 December 2020

On the specificity of antibody/antigen interactions: phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data

1 reference

12 December 2020

10.1016/S0006-3495(97)78266-3

Identifiers

DOI

1 reference

11 November 2017

1 reference

11 November 2017

1 reference

PMCID

1181139