(Q38647120)

5 September 2017

Geometric measures of large biomolecules: surface, volume, and pockets (English)

1 reference

5 September 2017

Paul Mach

1

1 reference

PMC publication ID

3188685

5 September 2017

Patrice Koehl

series ordinal

2

1 reference

5 September 2017

8 August 2011

1 reference

Journal of Computational Chemistry

5 September 2017

1 reference

5 September 2017

32

1 reference

5 September 2017

14

1 reference

5 September 2017

3023-3038

1 reference

VIPERdb2: an enhanced and web API enabled relational database for structural virology

5 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

MolAxis: a server for identification of channels in macromolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

PocketPicker: analysis of ligand binding-sites with shape descriptors.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Analytical approximation to the accessible surface area of proteins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

The weighted-volume derivative of a space-filling diagram

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Placement of the structural proteins in Sindbis virus

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Differences between pair and bulk hydrophobic interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Structure of the 30S ribosomal subunit

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

The interpretation of protein structures: Estimation of static accessibility

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Solvation energy in protein folding and binding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Fast prediction and visualization of protein binding pockets with PASS.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

Pairwise calculation of protein solvent-accessible surface areas

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188685

A method to compute the volume of a molecule

31 August 2018

1 reference

Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)

21 January 2018

1 reference

Computation of molecular volume

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

A Gaussian Description of Molecular Shape

21 January 2018

1 reference

Incremental topological flipping works for regular triangulations

21 January 2018

1 reference

Three-dimensional alpha shapes

21 January 2018

1 reference

Molecular surface area and hydrophobic effect

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21823134

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/JCC.21884

1 reference

5 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3188685

5 September 2017

PubMed publication ID

21823134

1 reference

PMC publication ID

3188685