(Q28484175)

April 2022 Public Data File from Crossref

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A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Application of fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design to identify novel microM leads for the development of nM BACE-1 (beta-site APP cleaving enzyme 1) inhibitors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

2-Amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (beta-site APP cleaving enzyme): Use of structure based design to convert a micromolar hit into a nanomolar lead

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Application of fragment screening by X-ray crystallography to beta-secretase

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Development and validation of a genetic algorithm for flexible docking

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Automated docking of flexible ligands: applications of AutoDock

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Surflex-Dock: Docking benchmarks and real-world application

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

The β-secretase enzyme BACE1 as a therapeutic target for Alzheimer's disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Beta-secretase as a target for Alzheimer's disease drug discovery: an overview of in vitro methods for characterization of inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Docking-based virtual screening for ligands of G protein-coupled receptors: not only crystal structures but also in silico models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

The transcriptionally active amyloid precursor protein (APP) intracellular domain is preferentially produced from the 695 isoform of APP in a {beta}-secretase-dependent pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Protein thermostability calculations using alchemical free energy simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Docking-based virtual screening: recent developments.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

beta-Secretase as a therapeutic target for Alzheimer's disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Homophilic interactions of the amyloid precursor protein (APP) ectodomain are regulated by the loop region and affect beta-secretase cleavage of APP.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Scoring functions and enrichment: a case study on Hsp90.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Virtual screening using binary kernel discrimination: analysis of pesticide data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Virtual screening for beta-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Improving structure-based virtual screening by multivariate analysis of scoring data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

A specific mechanism of nonspecific inhibition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Structure-based virtual screening: an overview

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

How does consensus scoring work for virtual library screening? An idealized computer experiment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Free energy via molecular simulation: applications to chemical and biomolecular systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Niemann-Pick type C cells show cholesterol dependent decrease of APP expression at the cell surface and its increased processing through the beta-secretase pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Effect of detergent on "promiscuous" inhibitors

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Combined SVM-based and docking-based virtual screening for retrieving novel inhibitors of c-Met

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Comparative assessment of scoring functions on a diverse test set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

General and targeted statistical potentials for protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Comparative evaluation of 11 scoring functions for molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Insights on the role of (dis)order from protein-protein interaction linear free-energy relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

A docking score function for estimating ligand-protein interactions: application to acetylcholinesterase inhibition

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Virtual screening using protein-ligand docking: avoiding artificial enrichment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Principal component and linear discriminant analyses of free amino acids and biogenic amines in hungarian wines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Impact of ligand protonation on virtual screening against beta-secretase (BACE1).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Apo and inhibitor complex structures of BACE (beta-secretase).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Automated docking with grid-based energy evaluation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Evaluation of binary QSAR models derived from LUDI and MOE scoring functions for structure based virtual screening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Chris Lipinski discusses life and chemistry after the Rule of Five

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

In silico discovery of beta-secretase inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Comparison of ranking methods for virtual screening in lead-discovery programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

In Silico Binding Free Energy Predictability by Using the Linear Interaction Energy (LIE) Method: Bromobenzimidazole CK2 Inhibitors as a Case Study

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0038086

Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3372491

Principal component analysis of measured quantities during degradation of hydroperoxides in oxidized vegetable oils

27 November 2018

1 reference

12 December 2020

A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities

1 reference

12 December 2020

Discovering severe acute respiratory syndrome coronavirus 3CL protease inhibitors: virtual screening, surface plasmon resonance, and fluorescence resonance energy transfer assays

1 reference

12 December 2020

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

1 reference

12 December 2020

LigScore: a novel scoring function for predicting binding affinities

1 reference

12 December 2020

Principal component analysis of trace elements in Serbian wheat

1 reference

12 December 2020