(Q41812957)

12 October 2017

Minimalist explicit solvation models for surface loops in proteins (English)

1 reference

12 October 2017

Ronald P White

1

1 reference

PMCID

1851699

12 October 2017

Hagai Meirovitch

series ordinal

2

1 reference

12 October 2017

1 January 2006

1 reference

Journal of Chemical Theory and Computation

12 October 2017

1 reference

12 October 2017

2

1 reference

12 October 2017

4

1 reference

12 October 2017

1135-1151

1 reference

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

A hierarchical approach to all-atom protein loop prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Dynamics of protein and peptide hydration

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Water rotational relaxation and diffusion in hydrated lysozyme

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Residence times of water molecules in the hydration sites of myoglobin

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Model building by comparison at CASP3: using expert knowledge and computer automation.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

6 June 2018

Long loops in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Protein hydration elucidated by molecular dynamics simulation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Evaluation of the conformational free energies of loops in proteins.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Omega loops: nonregular secondary structures significant in protein function and stability

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Modelling mutations and homologous proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Loops in globular proteins: a novel category of secondary structure

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Conformations of immunoglobulin hypervariable regions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Accurate simulation of protein dynamics in solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Modeling the anti-CEA antibody combining site by homology and conformational search

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Atomic solvation parameters applied to molecular dynamics of proteins in solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Dynamics of folded proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Towards molecular dynamics simulation of large proteins with a hydration shell at constant pressure.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

An automated classification of the structure of protein loops.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

A global taxonomy of loops in globular proteins.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

Optimization of solvation models for predicting the structure of surface loops in proteins

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851699

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

3 November 2018

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

Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins

1 reference

12 December 2020

Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020

A critical assessment of comparative molecular modeling of tertiary structures of proteins

1 reference

12 December 2020

Molecular dynamics simulation of solvated azurin: Correlation between surface solvent accessibility and water residence times

1 reference

12 December 2020

Protein hydration in aqueous solution

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

Backbone entropy of loops as a measure of their flexibility: application to a ras protein simulated by molecular dynamics

1 reference

12 December 2020

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

1 reference

12 December 2020

Prediction of loop geometries using a generalized born model of solvation effects

1 reference

12 December 2020

Mechanisms of antibody binding to a protein

1 reference

12 December 2020

Dynamics of hydration in hen egg white lysozyme

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT0503217

1 reference

12 October 2017

1 reference

12 October 2017

1 reference

PMCID

1851699