(Q42847562)

8 November 2017

Analysis of knowledge-based protein-ligand potentials using a self-consistent method (English)

1 reference

8 November 2017

Eugene I. Shakhnovich

series ordinal

3

object named as

Shakhnovich EI

1 reference

8 November 2017

Shimada J

1

1 reference

PMCID

2144609

8 November 2017

Ishchenko AV

series ordinal

2

1 reference

8 November 2017

1 April 2000

1 reference

8 November 2017

1 reference

8 November 2017

9

1 reference

8 November 2017

765-775

1 reference

8 November 2017

4

1 reference

Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design

8 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Structural analysis of inhibitor binding to human carbonic anhydrase II

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

How to derive a protein folding potential? A new approach to an old problem

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Structure-derived potentials and protein simulations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Computational methods to predict binding free energy in ligand-receptor complexes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Exploring conformational space with a simple lattice model for protein structure

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Pseudodihedrals: simplified protein backbone representation with knowledge-based energy

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Optimal protein-folding codes from spin-glass theory

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Protein tertiary structure recognition using optimized Hamiltonians with local interactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Statistical potentials extracted from protein structures: how accurate are they?

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144609

Why do protein architectures have Boltzmann-like statistics?

16 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/10794420

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Helmholtz free energies of atom pair interactions in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/10794420

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1110/PS.9.4.765

1 reference

8 November 2017

1 reference

8 November 2017

1 reference

PMCID

2144609