Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery (Q36416631)

14 August 2017

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title

Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery (English)

1 reference

14 August 2017

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1 reference

Vijayalakshmi Chelliah

Vijayalakshmi Chelliah

5

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Owen R Davies

Owen Davies

8

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David F Burke

David Burke

9

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Tom Blundell

1

Tom L Blundell

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14 August 2017

Catherine Louise Worth

6

Catherine L Worth

1 reference

14 August 2017

4

Suzanne Brewerton

1 reference

14 August 2017

Bancinyane L Sibanda

2

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14 August 2017

Rinaldo Wander Montalvão

3

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14 August 2017

Nicholas J Harmer

7

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14 August 2017

language of work or name

English

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publication date

1 March 2006

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14 August 2017

11

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Philosophical Transactions of the Royal Society B

inferred from page(s)

published in

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14 August 2017

361

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14 August 2017

1467

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14 August 2017

413-423

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Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation.

14 August 2017

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

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Comprehensive survey of combinatorial library synthesis: 2003.

30 September 2017

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Virtual screening in lead discovery and optimization.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Fragment-based lead discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Ligand efficiency: a useful metric for lead selection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Crystallography, NMR and virtual screening: integrated tools for drug discovery.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Facilities and methods for the high-throughput crystal structural analysis of human proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Structure-based virtual screening: an overview

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Insights into DNA recombination from the structure of a RAD51-BRCA2 complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Integration of virtual and high-throughput screening

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A new test set for validating predictions of protein-ligand interaction.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A review of protein-small molecule docking methods

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Lead discovery using molecular docking

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Structure-based screening of low-affinity compounds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Combinatorial chemistry and high-throughput screening in drug discovery: different strategies and formats

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Evolutionary predictions of binding surfaces and interactions.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Crystal structure of an Xrcc4-DNA ligase IV complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

High-throughput docking for lead generation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Discovering novel ligands for macromolecules using X-ray crystallographic screening

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Science, art and drug discovery: a personal perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Model building by comparison at CASP3: using expert knowledge and computer automation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

The SHAPES strategy: an NMR-based approach for lead generation in drug discovery.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Mapping of protein-protein interactions within the DNA-dependent protein kinase complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

High-throughput screening of historic collections: observations on file size, biological targets, and file diversity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

The PROSITE database, its status in 1999

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Discovering high-affinity ligands for proteins: SAR by NMR

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Comparative protein modelling by satisfaction of spatial restraints

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Ku80: product of the XRCC5 gene and its role in DNA repair and V(D)J recombination

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Protein structure--based drug design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

DNA-dependent kinase (p350) as a candidate gene for the murine SCID defect

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Loss of the catalytic subunit of the DNA-dependent protein kinase in DNA double-strand-break-repair mutant mammalian cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Prediction of protein secondary structure and active sites using the alignment of homologous sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A structural model for the retroviral proteases.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A new approach to protein fold recognition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Domain closure in mitochondrial aspartate aminotransferase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Compounds designed to fit a site of known structure in human haemoglobin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Restoration of X-ray resistance and V(D)J recombination in mutant cells by Ku cDNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Structural analysis of DNA-PKcs: modelling of the repeat units and insights into the detailed molecular architecture

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Three-dimensional structure analysis of PROSITE patterns

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Protein clefts in molecular recognition and function

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Fragment-based lead discovery using X-ray crystallography.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Distinguishing structural and functional restraints in evolution in order to identify interaction sites

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Fragment-Based Drug Discovery

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Assessment of progress over the CASP experiments

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Identification of related proteins on family, superfamily and fold level.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

The interaction of human haemoglobin with allosteric effectors as a model for drug-receptor interactions

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Three-dimensional structure, specificity and catalytic mechanism of renin

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1609333

A guide to drug discovery: The role of the medicinal chemist in drug discovery — then and now

21 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1098%2FRSTB.2005.1800

Signalling the fat controller

21 January 2018

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Crossref

https://api.crossref.org/works/10.1098%2FRSTB.2005.1800

Sequence and structure conservation in a protein core

21 January 2018

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12 December 2020

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures

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Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition

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Analysis of the steric strain in the polypeptide backbone of protein molecules

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Protein structural alignments and functional genomics

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Structural genomics. Tapping DNA for structures produces a trickle

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12 December 2020

Purification and characterization of the double-stranded DNA-activated protein kinase, DNA-PK, from human placenta

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Identifiers

DOI

10.1098/RSTB.2005.1800

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

16524830

1 reference