The importance of discerning shape in molecular pharmacology (Q33789461)

29 July 2017

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title

The importance of discerning shape in molecular pharmacology (English)

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29 July 2017

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29 July 2017

Matthew D Krasowski

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Sandhya Kortagere

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29 July 2017

publication date

31 January 2009

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Trends in Pharmacological Sciences

29 July 2017

published in

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29 July 2017

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29 July 2017

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29 July 2017

page(s)

138-147

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Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening

29 July 2017

cites work

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Shape signatures: new descriptors for predicting cardiotoxicity in silico

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Multi-dimensional QSAR in drug discovery

4 July 2018

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4 July 2018

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4 July 2018

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Selection of molecules based on shape and electrostatic similarity: proof of concept of "electroforms".

4 July 2018

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

4 July 2018

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4 July 2018

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Drugs in other drugs: a new look at drugs as fragments

4 July 2018

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Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach

4 July 2018

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4 July 2018

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The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets

4 July 2018

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Three-dimensional computation of atom depth in complex molecular structures.

4 July 2018

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Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile salts

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain

4 July 2018

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Using ensembles to classify compounds for drug discovery

4 July 2018

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Electronic van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

A novel shape-feature based approach to virtual library screening

4 July 2018

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Evaluation of a novel shape-based computational filter for lead evolution: application to thrombin inhibitors

4 July 2018

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Molecules within molecules: recognition through self-assembly

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

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

4 July 2018

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The use of bioisosteric groups in lead optimization

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Crystal structure of a cocaine-binding antibody

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

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

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

The orphan nuclear receptor SXR coordinately regulates drug metabolism and efflux

4 July 2018

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QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).

4 July 2018

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Development and validation of a genetic algorithm for flexible docking

4 July 2018

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Bioisosterism as a molecular diversity descriptor: steric fields of single "topomeric" conformers.

4 July 2018

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Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors

4 July 2018

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

4 July 2018

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Automated docking of substrates to proteins by simulated annealing

4 July 2018

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"Soft docking": matching of molecular surface cubes

4 July 2018

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Distance geometry approach to rationalizing binding data

4 July 2018

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Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Fast, sensitive and cost-effective detection of nerve agents in the gas phase using a portable instrument and an electrochemical biosensor

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Tracking the chiral recognition of adsorbed dipeptides at the single-molecule level

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Ultrafast shape recognition to search compound databases for similar molecular shapes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Three-dimensional quantitative structure-activity relationship analysis of human CYP51 inhibitors

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Travel depth, a new shape descriptor for macromolecules: application to ligand binding

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Insights for Human Ether-a-Go-Go-Related Gene Potassium Channel Inhibition Using Recursive Partitioning and Kohonen and Sammon Mapping Techniques

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI).

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Structural disorder in the complex of human pregnane X receptor and the macrolide antibiotic rifampicin

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Enrichment of ligands for the serotonin receptor using the Shape Signatures approach

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Shape signatures: a new approach to computer-aided ligand- and receptor-based drug design

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

New developments in PEST shape/property hybrid descriptors.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Transferable atom equivalent multicentered multipole expansion method.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Three-dimensional structure-activity relationship modeling of cocaine binding to two monoclonal antibodies by comparative molecular field analysis

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

A new class of molecular shape descriptors. 1. Theory and properties.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Local intersection volume: a new 3D descriptor applied to develop a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Prospective identification of biologically active structures by topomer shape similarity searching

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Comparison of Shape-Matching and Docking as Virtual Screening Tools

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

30 October 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2854656

Partial molecular alignment via local structure analysis

30 October 2018

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12 December 2020

Bacterial ribonuclease P reaction is affected by substrate shape and magnesium ion concentration

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12 December 2020

Specificity of substrate recognition by Pseudomonas fluorescens N3 dioxygenase. The role of the oxidation potential and molecular geometry

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12 December 2020

Path-space ratio as a molecular shape descriptor of polymer conformation

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12 December 2020

Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface

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12 December 2020

A general QSAR for dihydrofolate reductase inhibition by 2,4-diaminotriazines based upon molecular shape analysis

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12 December 2020

New quantum mechanics-based three-dimensional molecular descriptors for use in QSSR approaches: application to asymmetric catalysis

1 reference

12 December 2020

10.1016/J.TIPS.2008.12.001

Identifiers

DOI

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29 July 2017

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29 July 2017

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