(Q33247681)

24 July 2017

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title

Virtual ligand screening: strategies, perspectives and limitations (English)

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24 July 2017

Gerhard Klebe

1

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24 July 2017

1 July 2006

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24 July 2017

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24 July 2017

11

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24 July 2017

580-594

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24 July 2017

13-14

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Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

24 July 2017

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12 December 2020

Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations.

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12 December 2020

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

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12 December 2020

Knowledge-based scoring function to predict protein-ligand interactions.

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12 December 2020

A ‘Rule of Three’ for fragment-based lead discovery?

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12 December 2020

Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis

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12 December 2020

Structure-based virtual screening: an overview

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12 December 2020

Testing a flexible-receptor docking algorithm in a model binding site

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12 December 2020

The art and practice of structure-based drug design: A molecular modeling perspective

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12 December 2020

Detailed analysis of scoring functions for virtual screening

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12 December 2020

Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

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12 December 2020

Fragment-Based Drug Discovery

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12 December 2020

Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials

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12 December 2020

A new grammar for drug discovery

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12 December 2020

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

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12 December 2020

Comparing protein-ligand docking programs is difficult.

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12 December 2020

Structural parameterization of the binding enthalpy of small ligands

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12 December 2020

Modeling water molecules in protein-ligand docking using GOLD.

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12 December 2020

Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.

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12 December 2020

Feature trees: a new molecular similarity measure based on tree matching.

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12 December 2020

Docking flexible ligands to macromolecular receptors by molecular shape

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12 December 2020

Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naïve Bayesian classifier: limitations of the descriptor and the importance of balanced chemistry in training and test sets

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12 December 2020

Development and validation of a genetic algorithm for flexible docking

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12 December 2020

Virtual screening in lead discovery and optimization.

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12 December 2020

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

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12 December 2020

FlexE: efficient molecular docking considering protein structure variations.

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12 December 2020

Accommodating protein flexibility in computational drug design

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12 December 2020

Pharmacophore modeling and three-dimensional database searching for drug design using catalyst

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12 December 2020

DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction

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12 December 2020

How many leads from HTS? - Comment

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12 December 2020

Lead discovery using molecular docking

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12 December 2020

Chris Lipinski discusses life and chemistry after the Rule of Five.

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12 December 2020

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

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12 December 2020

Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.

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12 December 2020

Understanding protein-ligand interactions: the price of protein flexibility

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12 December 2020

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

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12 December 2020

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

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12 December 2020

Comparative evaluation of 11 scoring functions for molecular docking

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12 December 2020

Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease

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12 December 2020

Virtual screening of chemical libraries

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12 December 2020

Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods

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12 December 2020

Docking into knowledge-based potential fields: a comparative evaluation of DrugScore

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12 December 2020

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

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12 December 2020

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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12 December 2020

A fast flexible docking method using an incremental construction algorithm.

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12 December 2020

Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions

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12 December 2020

How many leads from HTS?

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12 December 2020

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

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12 December 2020

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

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12 December 2020

All are not equal: a benchmark of different homology modeling programs

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12 December 2020

Pharmacophore-based molecular docking to account for ligand flexibility

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12 December 2020

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

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12 December 2020

Integration of virtual screening into the drug discovery process

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12 December 2020

Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor

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12 December 2020

Molecular docking to ensembles of protein structures

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12 December 2020

Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design

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12 December 2020

High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate

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12 December 2020

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

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12 December 2020

Comparing Performance of Computational Tools for Combinatorial Library Design

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12 December 2020

High-throughput docking as a source of novel drug leads

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12 December 2020

ADMET in silico modelling: towards prediction paradise?

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12 December 2020

ZINC--a free database of commercially available compounds for virtual screening

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12 December 2020

Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition

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12 December 2020

McMaster University data-mining and docking competition: computational models on the catwalk

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12 December 2020

Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds

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12 December 2020

From the analyst's couch. Trends in development cycles

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12 December 2020

Ligand docking to proteins with discrete side-chain flexibility.

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12 December 2020

Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin.

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12 December 2020

Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock

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12 December 2020

Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions

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12 December 2020

Utilising structural knowledge in drug design strategies: applications using Relibase.

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12 December 2020

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

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12 December 2020

Flexible docking under pharmacophore type constraints

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12 December 2020

Recent development and application of virtual screening in drug discovery: an overview

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12 December 2020

Here be dragons: docking and screening in an uncharted region of chemical space

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12 December 2020

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

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12 December 2020

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12 December 2020

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation

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12 December 2020

Evaluating the high-throughput screening computations

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12 December 2020

Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case

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12 December 2020

DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.

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12 December 2020

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

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12 December 2020

Experimental screening of dihydrofolate reductase yields a "test set" of 50,000 small molecules for a computational data-mining and docking competition

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12 December 2020

High-throughput docking for lead generation

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12 December 2020

Docking: successes and challenges

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12 December 2020

Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening

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12 December 2020

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12 December 2020

Docking and scoring in virtual screening for drug discovery: methods and applications

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12 December 2020

Virtual screening methods that complement HTS.

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12 December 2020

Improving binding mode predictions by docking into protein-specifically adapted potential fields

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12 December 2020

Target-biased scoring approaches and expert systems in structure-based virtual screening

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12 December 2020

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12 December 2020

Assessing scoring functions for protein-ligand interactions.

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12 December 2020

Virtual screening in structure-based drug discovery

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12 December 2020

Docking ligands onto binding site representations derived from proteins built by homology modelling.

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12 December 2020

Virtual exploration of the small-molecule chemical universe below 160 Daltons

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12 December 2020

Comparison of automated docking programs as virtual screening tools

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12 December 2020

ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.

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12 December 2020

Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4

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12 December 2020

Molecular recognition and docking algorithms

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12 December 2020

Fragment-based lead discovery

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12 December 2020

Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.

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12 December 2020

A geometric approach to macromolecule-ligand interactions

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12 December 2020

Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes

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12 December 2020

Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity

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12 December 2020

Current trends in lead discovery: are we looking for the appropriate properties?

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12 December 2020

A bioavailability score.

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12 December 2020

pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design

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12 December 2020

Implications of protein flexibility for drug discovery

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12 December 2020

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

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12 December 2020

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

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12 December 2020

Utility of homology models in the drug discovery process.

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12 December 2020

Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model

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12 December 2020

Evaluation of the CASP2 docking section

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12 December 2020

Druggability indices for protein targets derived from NMR-based screening data

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12 December 2020

Chemical feature-based pharmacophores and virtual library screening for discovery of new leads.

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12 December 2020

Hit and lead generation: beyond high-throughput screening

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12 December 2020

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

1 reference

12 December 2020

10.1016/J.DRUDIS.2006.05.012

Identifiers

DOI

1 reference

24 July 2017

1 reference

PubMed ID

16793526