Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines (Q36165757)

12 August 2017

Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines (English)

1 reference

12 August 2017

2

H A Scheraga

1 reference

12 August 2017

J Y Trosset

1

1 reference

PMCID

20920

12 August 2017

language of work or name

English

0 references

publication date

1 July 1998

1 reference

Proceedings of the National Academy of Sciences of the United States of America

12 August 2017

1 reference

12 August 2017

95

1 reference

12 August 2017

14

1 reference

12 August 2017

8011-8015

1 reference

Modelling protein docking using shape complementarity, electrostatics and biochemical information

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Development and validation of a genetic algorithm for flexible docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

PUZZLE: a new method for automated protein docking based on surface shape complementarity.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Automated docking of substrates to proteins by simulated annealing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

The refined 1.9-Å X-ray crystal structure of d-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Molecular docking using surface complementarity.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Monte Carlo docking with ubiquitin

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Distance-constrained molecular docking by simulated annealing.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

"Soft docking": matching of molecular surface cubes

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Protein docking and complementarity

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

A robust and efficient automated docking algorithm for molecular recognition

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Monte Carlo docking of oligopeptides to proteins.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

A multiple-start Monte Carlo docking method.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Docking by least-squares fitting of molecular surface patterns

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

Molecular docking using shape descriptors

2 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Matching chemistry and shape in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

MONTY: a Monte Carlo approach to protein-DNA recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Molecular dynamics simulation of the docking of substrates to proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Low-resolution docking: prediction of complexes for underdetermined structures.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

A geometry-based suite of molecular docking processes.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=20920

A genetic algorithm based method for docking flexible molecules

23 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Fitting an inhibitor into the active site of thermolysin: a molecular dynamics case study

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Molecular dynamics simulations of the docking of substituted N5-deazapterins to dihydrofolate reductase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.95.14.8011

Docking enzyme-inhibitor complexes using a preference-based free-energy surface

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9653131

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.95.14.8011

1 reference

12 August 2017

0 references

1 reference

12 August 2017

1 reference

PMCID

20920