Are proteins well-packed? (Q34176053)

31 July 2017

Are proteins well-packed? (English)

1 reference

31 July 2017

2

Dill KA

1 reference

31 July 2017

Liang J

1

1 reference

PubMed ID

11463623

31 July 2017

language of work or name

English

0 references

publication date

1 August 2001

1 reference

31 July 2017

1 reference

31 July 2017

81

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31 July 2017

751-766

1 reference

31 July 2017

2

1 reference

Detection, delineation, measurement and display of cavities in macromolecular structures

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Protein folding: from the levinthal paradox to structure prediction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

The packing density in proteins: standard radii and volumes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Network Approach to Void Percolation in a Pack of Unequal Spheres

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Hydration structure of antithrombin conformers and water transfer during reactive loop insertion

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Computation of molecular electrostatics with boundary element methods

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Packing at the protein-water interface

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Active barnase variants with completely random hydrophobic cores

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Energetics of protein structure.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of ubiquitin unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Intramolecular cavities in globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

An analysis of packing in the protein folding problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of unfolding of the all beta-sheet protein interleukin-1 beta.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Enlarged representative set of protein structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of barnase unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Side-chain entropy and packing in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Cavities and packing at protein interfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of BPTI folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Adiabatic compressibility of globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Principles that determine the structure of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

The interpretation of protein structures: Estimation of static accessibility

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

The interpretation of protein structures: Total volume, group volume distributions and packing density

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Internal cavities and buried waters in globular proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

A scanning calorimetric study of the thermal denaturation of the lysozyme of phage T4 and the Arg 96----His mutant form thereof

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

A very fast program for visualizing protein surfaces, channels and cavities.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Cavity search: an algorithm for the isolation and display of cavity-like binding regions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Solid model compounds and the thermodynamics of protein unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of unfolding of the alpha-amylase inhibitor tendamistat. Correlations between accessible surface area and heat capacity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Areas, volumes, packing and protein structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Papain denaturation is not a two-state transition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Energetics of ribonuclease T1 structure.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Volume changes on protein folding.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Thermodynamics of the thermal unfolding of eglin c in the presence and absence of guanidinium chloride.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301551

Series study of percolation moments in general dimension

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Structural invariants in protein folding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Analytical molecular surface calculation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Finding and filling protein cavities using cellular logic operations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

A Comparative Study of Peptide Models of the α-Domain of α-Lactalbumin, Lysozyme, and α-Lactalbumin/Lysozyme Chimeras Allows the Elucidation of Critical Factors That Contribute to the Ability to Form Stable Partially Folded States†

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

The union of balls and its dual shape

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

On the definition and the construction of pockets in macromolecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Three-dimensional alpha shapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Incremental topological flipping works for regular triangulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Volume occupation, environment and accessibility in proteins. The problem of the protein surface

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Calculation of protein volumes: an alternative to the Voronoi procedure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Randomized incremental construction of Delaunay and Voronoi diagrams

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Alternative packing arrangements in the hydrophobic core of λrepresser

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Universality and cluster structures in continuum models of percolation with two different radius distributions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Pepsinogen denaturation is not a two‐state transition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

Counting polyominoes: Yet another attack

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975739-6

10.1016/S0006-3495(01)75739-6

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

11463623