Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase (Q33532330)

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Language	Label	Description	Also known as
English	Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase	scientific article

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase (English)

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

transmembrane protein

0 references

endoplasmic reticulum

0 references

author name string

Michael Lape

1

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

Christopher Elam

2

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

Stefan Paula

3

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

publication date

4 February 2010

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

Biophysical Chemistry

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

150

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

1-3

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

88-97

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

The role of dynamic conformational ensembles in biomolecular recognition

1 reference

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Managing protein flexibility in docking and its applications

1 reference

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21 June 2018

Structure-based virtual screening for novel inhibitors of the sarco/endoplasmic reticulum calcium ATPase and their experimental evaluation

1 reference

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The structural basis of calcium transport by the calcium pump

1 reference

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21 June 2018

Molecular determinants of sarco/endoplasmic reticulum calcium ATPase inhibition by hydroquinone-based compounds

1 reference

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21 June 2018

Comparison of topological, shape, and docking methods in virtual screening.

1 reference

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21 June 2018

Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets

1 reference

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21 June 2018

Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors

1 reference

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A semiempirical free energy force field with charge-based desolvation

1 reference

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Implications of protein conformational diversity for binding and development of new biological active compounds.

1 reference

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Application of a Theory of Enzyme Specificity to Protein Synthesis

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Natural products as starting materials for development of second-generation SERCA inhibitors targeted towards prostate cancer cells

1 reference

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Investigation of the binding mode of (-)-meptazinol and bis-meptazinol derivatives on acetylcholinesterase using a molecular docking method

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New strategies for the medical treatment of prostate cancer

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Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)

1 reference

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21 June 2018

Transport mechanism of the sarcoplasmic reticulum Ca2+ -ATPase pump

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Comparing protein-ligand docking programs is difficult.

1 reference

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21 June 2018

Comparison of automated docking programs as virtual screening tools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Evaluation and application of multiple scoring functions for a virtual screening experiment

1 reference

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21 June 2018

Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Gaussian docking functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

1 reference

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A review of protein-small molecule docking methods

1 reference

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21 June 2018

Structural changes in the calcium pump accompanying the dissociation of calcium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

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Accommodating protein flexibility in computational drug design

1 reference

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

1 reference

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Development and validation of a genetic algorithm for flexible docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Computational methods for biomolecular docking.

1 reference

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21 June 2018

Structural organization, ion transport, and energy transduction of P-type ATPases

1 reference

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A geometric approach to macromolecule-ligand interactions

1 reference

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Structural dynamics of yeast hexokinase during catalysis

1 reference

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Automated docking of substrates to proteins by simulated annealing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

Thapsigargine and thapsigargicine, two new histamine liberators from Thapsia garganica L.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

21 June 2018

High quality binding modes in docking ligands to proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

Critical assessment of the automated AutoDock as a new docking tool for virtual screening.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

General and targeted statistical potentials for protein-ligand interactions.

1 reference

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Applying linear interaction energy method for rational design of noncompetitive allosteric inhibitors of the sarco- and endoplasmic reticulum calcium-ATPase

1 reference

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Molecular determinants of thapsigargin binding by SERCA Ca2+-ATPase: a computational docking study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

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Multiple active site corrections for docking and virtual screening.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

Flexible docking using Tabu search and an empirical estimate of binding affinity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

A tool coming of age: thapsigargin as an inhibitor of sarco-endoplasmic reticulum Ca(2+)-ATPases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2885586

31 October 2018

Comparison of three tetramic acids and their ability to alter membrane function in cultured skeletal muscle cells and sarcoplasmic reticulum vesicles

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

On the inhibition mechanism of sarcoplasmic or endoplasmic reticulum Ca2+-ATPases by cyclopiazonic acid

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-Activity Relationships of Analogs of Thapsigargin Modified at O-11 and O-12

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Cyclopiazonic Acid Effect on Ca2+-Dependent Conformational States of the Sarcoplasmic Reticulum ATPase. Implication for the Enzyme Turnover†

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

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based on heuristic

inferred from PubMed ID database lookup

Cardiac sarcoplasmic reticulum Ca2+ pump as a target for benzoquinones

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interactions of Dihydroxybenzenes with the Ca2+-ATPase: Separate Binding Sites for Dihydroxybenzenes and Sesquiterpene Lactones

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Inhibition of the sarcoplasmic reticulum Ca2+ transport ATPase by thapsigargin at subnanomolar concentrations

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

https://pubmed.ncbi.nlm.nih.gov/20167416

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.BPC.2010.01.011

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

ResearchGate publication ID

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