List of works - David B Ascher

A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats

scientific article published on 06 March 2019

A Comprehensive Computational Platform to Guide Drug Development Using Graph-Based Signature Methods

scientific article published on 01 January 2020

A Computational Approach From Gene to Structure Analysis of the Human ABCA4 Transporter Involved in Genetic Retinal Diseases

scientific article

A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites

scientific article published on 01 September 2019

A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction

scientific article published on 19 June 2020

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors.

scientific article published on 5 May 2015

Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations

scientific article

Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy.

scientific article published on 25 April 2018

Anti-Aβ antibody target engagement: a response to Siemers et al.

scientific article published on 15 August 2014

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

scientific article

Assessment of the Urinary Microbiome in Children Younger Than 48 Months

scientific article published on 20 February 2020

Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

scientific article published on 04 January 2021

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.

scientific article

Clinical spectrum of Shiga toxin-producing Escherichia coli (STEC) in adults and children

scientific article

Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design.

scientific article published on June 2017

Combining structure and genomics to understand antimicrobial resistance

scientific article published on 29 October 2020

Comparison of fluconazole and nystatin oral suspensions for treatment of oral candidiasis in infants

scientific article

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae

scientific article published on 17 January 2020

Conjugation of 10 kDa Linear PEG onto Trastuzumab Fab' Is Sufficient to Significantly Enhance Lymphatic Exposure while Preserving in Vitro Biological Activity

scientific article published on 12 February 2016

Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH)

scientific article published on 09 November 2019

Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides.

scientific article published on 26 December 2014

Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein.

scientific article

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2.

scientific article

Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Abeta peptides associated with Alzheimer's disease.

scientific article published on 30 April 2008

Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β

scientific article

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair

scientific article published on 2 February 2017

DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage.

scientific article

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.

scientific article published on 14 May 2014

Definition of the immune evasion-replication interface of rabies virus P protein

scientific article published on 08 July 2021

Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase

scientific article

Dimeric but not monomeric α-lactalbumin potentiates apoptosis by up regulation of ATF3 and reduction of histone deacetylase activity in primary and immortalised cells

scientific article published on 10 February 2017

Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target?

scientific article

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations

scientific article published on 03 September 2020

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.

scientific article published in July 2018

EasyVS: a user friendly web based tool for molecule library selection and structure-based virtual screening

scientific article published on 12 May 2020

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

scientific article published on 29 May 2019

Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis

scientific article

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

scientific article

Exploring Protein Supersecondary Structure Through Changes in Protein Folding, Stability, and Flexibility

scientific article published on 01 January 2019

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges

scientific article published in 2024

Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

scientific article published on 09 September 2020

Familial STAG2 germline mutation defines a new human cohesinopathy

scientific article published on 20 March 2017

Flexibility and small pockets at protein-protein interfaces: New insights into druggability.

scientific article published on 7 February 2015

Fragment-Based Approach to Targeting Inosine-5'-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis.

scientific article

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

article

Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins.

scientific article published on August 2016

Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance.

scientific article published on April 2017

Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma.

scientific article

Glutathione transferase P1-1 as an arsenic drug-sequestering enzyme.

scientific article

HARP: a database of structural impacts of systematic missense mutations in drug targets of <i>Mycobacterium leprae</i>

scientific article published on 19 November 2020

HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase

scientific article published in 2022

Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU

scientific article published on 08 February 2019

Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations

scientific article published on 28 April 2019

Huntingtin Inclusions Trigger Cellular Quiescence, Deactivate Apoptosis, and Lead to Delayed Necrosis

scientific article

Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis

scientific article published on 01 October 2019

Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase

scientific article published on 20 August 2008

Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase

scientific article published in June 2008

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis

scientific article published on 01 January 2021

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.

scientific article

Kinact: a computational approach for predicting activating missense mutations in protein kinases.

scientific article published in July 2018

Known allosteric proteins have central roles in genetic disease

scientific article published on 09 February 2022

Local Content, Smartphones, and Digital Inclusion

Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein

scientific article

MTR-Viewer: identifying regions within genes under purifying selection

scientific article published on 01 July 2019

Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumor-burdened lymph nodes after intravenous and subcutaneous administration in rats

scientific article

Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health

scientific article

Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases

scientific article published in 2024

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.

scientific article

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites.

scientific article published on 28 October 2019

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

scientific article published on September 2017

PEGylated interferon displays differences in plasma clearance and bioavailability between male and female mice and between female immunocompetent C57Bl/6J and athymic nude mice

scientific article published on 5 March 2015

PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats but increases plasma clearance after subcutaneous administration.

scientific article

PEGylation of interferon α2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases.

scientific article

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.

scientific article

Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA.

scientific article

Practical lessons in murine thoracic lymph duct cannulations: observations in female and male mice across four different strains that impact on "cannulatability".

scientific article published on 23 December 2014

Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand

scientific article published on 01 January 2018

Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches

scientific article published on 22 October 2020

ProCarbDB: a database of carbohydrate-binding proteins

scientific article published on 01 January 2020

Publisher Correction: Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.

scientific article

Python Cookbook, 2nd Edition

Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain

scientific article published on 9 March 2011

Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation.

scientific article

SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity.

scientific article

SDM: a server for predicting effects of mutations on protein stability

scientific article published on 19 May 2017

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.

scientific article

Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases

scientific article published on 05 September 2018

Structural approaches to probing metal interaction with proteins

scientific article published on 03 March 2012

Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration

scientific article

Structure guided prediction of Pyrazinamide resistance mutations in pncA

scientific article published on 05 February 2020

Structure of the N-terminal domain of human thioredoxin-interacting protein ⬇️

scientific article published on February 16, 2013

Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase

scientific article published on 16 September 2021

Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation

scientific article published on 16 June 2011

Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH

scientific article published on 15 April 2019

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis

scientific article

The Presence, Persistence and Functional Properties of Plasmodium vivax Duffy Binding Protein II Antibodies Are Influenced by HLA Class II Allelic Variants

scientific article

The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after INTRATRACHEAL administration to rats

scientific article published on 22 August 2020

ThermoMutDB: a thermodynamic database for missense mutations

scientific article published on 23 October 2020

Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction

scientific article published on 01 August 2024

Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes SDHB, SDHC and SDHD.

scientific article published on 31 January 2018

Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy.

scientific article published on 25 March 2015

Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis

scientific article

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

scientific article published in Scientific Reports

Unveiling six potent and highly selective antileishmanial agents via the open source compound collection 'Pathogen Box' against antimony-sensitive and -resistant Leishmania braziliensis

scientific article published on 04 December 2020

Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma

scientific article published on 06 September 2019

Variation in Human Cytochrome P-450 Drug-Metabolism Genes: A Gateway to the Understanding of Plasmodium vivax Relapses

scientific article

Widespread remodeling of proteome solubility in response to different protein homeostasis stresses

scientific article published on 21 January 2020

dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction

scientific article published on 29 October 2019

mCSM-AB2: guiding rational antibody design using graph-based signatures

scientific article published on 01 March 2020

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures

scientific article published on 23 May 2016

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.

scientific article

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions

scientific article published on 01 July 2019

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance

scientific article

mCSM-membrane: predicting the effects of mutations on transmembrane proteins

scientific article published on 29 May 2020

mCSM: predicting the effects of mutations in proteins using graph-based signatures.

scientific article published on 26 November 2013

mmCSM-AB: guiding rational antibody engineering through multiple point mutations

scientific article published on 20 May 2020

mycoCSM: using graph-based signatures to identify safe potent hits against Mycobacteria

scientific article published on 02 July 2020

pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures.

scientific article published on 22 April 2015

List of works by David B Ascher

A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats

A Comprehensive Computational Platform to Guide Drug Development Using Graph-Based Signature Methods

A Computational Approach From Gene to Structure Analysis of the Human ABCA4 Transporter Involved in Genetic Retinal Diseases

A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites

A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors.

Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations

Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy.

Anti-Aβ antibody target engagement: a response to Siemers et al.

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

Assessment of the Urinary Microbiome in Children Younger Than 48 Months

Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.

Clinical spectrum of Shiga toxin-producing Escherichia coli (STEC) in adults and children

Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design.

Combining structure and genomics to understand antimicrobial resistance

Comparison of fluconazole and nystatin oral suspensions for treatment of oral candidiasis in infants

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae

Conjugation of 10 kDa Linear PEG onto Trastuzumab Fab' Is Sufficient to Significantly Enhance Lymphatic Exposure while Preserving in Vitro Biological Activity

Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH)

Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides.

Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein.

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2.

Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Abeta peptides associated with Alzheimer's disease.

Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair

DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage.

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.

Definition of the immune evasion-replication interface of rabies virus P protein

Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase

Dimeric but not monomeric α-lactalbumin potentiates apoptosis by up regulation of ATF3 and reduction of histone deacetylase activity in primary and immortalised cells

Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target?

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.

EasyVS: a user friendly web based tool for molecule library selection and structure-based virtual screening

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

Exploring Protein Supersecondary Structure Through Changes in Protein Folding, Stability, and Flexibility

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges

Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

Familial STAG2 germline mutation defines a new human cohesinopathy

Flexibility and small pockets at protein-protein interfaces: New insights into druggability.

Fragment-Based Approach to Targeting Inosine-5'-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis.

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins.

Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance.

Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma.

Glutathione transferase P1-1 as an arsenic drug-sequestering enzyme.

HARP: a database of structural impacts of systematic missense mutations in drug targets of <i>Mycobacterium leprae</i>

HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase

Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU

Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations

Huntingtin Inclusions Trigger Cellular Quiescence, Deactivate Apoptosis, and Lead to Delayed Necrosis

Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis

Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase

Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.

Kinact: a computational approach for predicting activating missense mutations in protein kinases.

Known allosteric proteins have central roles in genetic disease

Local Content, Smartphones, and Digital Inclusion

Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein

MTR-Viewer: identifying regions within genes under purifying selection

Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumor-burdened lymph nodes after intravenous and subcutaneous administration in rats

Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health

Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites.

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

PEGylated interferon displays differences in plasma clearance and bioavailability between male and female mice and between female immunocompetent C57Bl/6J and athymic nude mice

PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats but increases plasma clearance after subcutaneous administration.

PEGylation of interferon α2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases.

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.

Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA.

Practical lessons in murine thoracic lymph duct cannulations: observations in female and male mice across four different strains that impact on "cannulatability".

Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand

A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats