(Q34176053)

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Are proteins well-packed?

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scholarly article

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Europe PubMed Central

PubMed publication ID

31 July 2017

Are proteins well-packed? (English)

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Europe PubMed Central

PubMed publication ID

31 July 2017

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object named as

Dill KA

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Europe PubMed Central

PubMed publication ID

31 July 2017

author name string

Liang J

1

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Europe PubMed Central

PubMed publication ID

31 July 2017

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publication date

1 August 2001

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Europe PubMed Central

PubMed publication ID

31 July 2017

Biophysical Journal

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Europe PubMed Central

PubMed publication ID

31 July 2017

81

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Europe PubMed Central

PubMed publication ID

31 July 2017

2

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

751-766

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

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

1 reference

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

5 July 2018

Protein folding: from the levinthal paradox to structure prediction

1 reference

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

5 July 2018

The packing density in proteins: standard radii and volumes.

1 reference

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

5 July 2018

Network Approach to Void Percolation in a Pack of Unequal Spheres

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Computation of molecular electrostatics with boundary element methods

1 reference

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

5 July 2018

Packing at the protein-water interface

1 reference

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

5 July 2018

Active barnase variants with completely random hydrophobic cores

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Energetics of protein structure.

1 reference

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

5 July 2018

Thermodynamics of ubiquitin unfolding

1 reference

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

5 July 2018

Intramolecular cavities in globular proteins

1 reference

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

5 July 2018

An analysis of packing in the protein folding problem

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Enlarged representative set of protein structures

1 reference

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

5 July 2018

Thermodynamics of barnase unfolding

1 reference

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

5 July 2018

Side-chain entropy and packing in proteins

1 reference

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

5 July 2018

Cavities and packing at protein interfaces

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Thermodynamics of BPTI folding

1 reference

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

5 July 2018

Adiabatic compressibility of globular proteins

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Principles that determine the structure of proteins

1 reference

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

5 July 2018

The interpretation of protein structures: Estimation of static accessibility

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Internal cavities and buried waters in globular proteins.

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

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

1 reference

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

5 July 2018

Solid model compounds and the thermodynamics of protein unfolding

1 reference

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

5 July 2018

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

1 reference

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

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

1 reference

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1 reference

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5 July 2018

Papain denaturation is not a two-state transition

1 reference

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

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Energetics of ribonuclease T1 structure.

1 reference

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Volume changes on protein folding.

1 reference

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

28 October 2018

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

1 reference

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

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Series study of percolation moments in general dimension

1 reference

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Structural invariants in protein folding

1 reference

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7 January 2021

Analytical molecular surface calculation

1 reference

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Finding and filling protein cavities using cellular logic operations

1 reference

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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†

1 reference

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7 January 2021

The union of balls and its dual shape

1 reference

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

7 January 2021

On the definition and the construction of pockets in macromolecules

1 reference

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

7 January 2021

Three-dimensional alpha shapes

1 reference

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

7 January 2021

Incremental topological flipping works for regular triangulations

1 reference

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

7 January 2021

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

1 reference

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

7 January 2021

Calculation of protein volumes: an alternative to the Voronoi procedure

1 reference

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7 January 2021

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

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7 January 2021

Randomized incremental construction of Delaunay and Voronoi diagrams

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7 January 2021

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

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7 January 2021

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7 January 2021

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

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7 January 2021

Pepsinogen denaturation is not a two‐state transition

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7 January 2021

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

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7 January 2021

Counting polyominoes: Yet another attack

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7 January 2021

Identifiers

10.1016/S0006-3495(01)75739-6

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

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