David Ascher

mCSM-AB2: Guiding Rational Antibody Design Using Graph-Based Signatures.

Yoochan Myung, Carlos HM Rodrigues, David B Ascher, Douglas EV Pires

Journal article  |  2020  |  Bioinformatics

MOTIVATION: A lack of accurate computational tools to guide rational mutagenesis has made affinity maturation a recurrent challeng..

Structure guided prediction of Pyrazinamide resistance mutations in pncA

Malancha Karmakar, Carlos HM Rodrigues, Kristy Horan, Justin T Denholm, David B Ascher

Journal article  |  2020  |  Scientific Reports

Pyrazinamide plays an important role in tuberculosis treatment; however, its use is complicated by side-effects and challenges wit..

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

Xiaojing Sui, Douglas EV Pires, Angelique R Ormsby, Dezerae Cox, Shuai Nie, Giulia Vecchi, Michele Vendruscolo, David B Ascher, Gavin E Reid, Danny M Hatters

Journal article  |  2020  |  Proceedings of the National Academy of Sciences

The accumulation of protein deposits in neurodegenerative diseases has been hypothesized to depend on a metastable subproteome vul..

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

Jean Pierre Bayley, Birke Bausch, Johannes Adriaan Rijken, Leonie Theresia van Hulsteijn, Jeroen C Jansen, David Ascher, Douglas Eduardo Valente Pires, Frederik J Hes, Erik F Hensen, Eleonora PM Corssmit, Peter Devilee, Hartmut PH Neumann

Journal article  |  2020  |  Journal of Medical Genetics

BACKGROUND: Pathogenic germline variants in subunits of succinate dehydrogenase (SDHB, SDHC and SDHD) are broadly associated with ..

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

Ana Trapero, Angela Pacitto, Daniel Shiu-Hin Chan, Chris Abell, Tom L Blundell, David B Ascher, Anthony G Coyne

Journal article  |  2020  |  Bioorganic & Medicinal Chemistry Letters

Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in nucleotide biosynthesis. Because of its criti..

ProCarbDB: a database of carbohydrate-binding proteins

Liviu Copoiu, Pedro HM Torres, David B Ascher, Tom L Blundell, Sony Malhotra

Journal article  |  2020  |  Nucleic Acids Research

Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, toge..

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

Nidhi Jatana, David B Ascher, Douglas E Pires, Rajesh S Gokhale, Lipi Thukral

Journal article  |  2020  |  Autophagy

Autophagy is a conserved adaptive cellular pathway essential to maintain a variety of physiological functions. Core components of ..

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

Sundeep Chaitanya Vedithi, Carlos HM Rodrigues, Stephanie Portelli, Marcin J Skwark, Madhusmita Das, David B Ascher, Tom L Blundell, Sony Malhotra

Journal article  |  2020  |  Computational and Structural Biotechnology Journal

Rifampin resistance in leprosy may remain undetected due to the lack of rapid and effective diagnostic tools. A quick and reliable..

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

Douglas EV Pires, Stephanie Portelli, Pâmela M Rezende, Wandré NP Veloso, Joicymara S Xavier, Malancha Karmakar, Yoochan Myung, João PV Linhares, Carlos HM Rodrigues, Michael Silk, David B Ascher

Journal article  |  2020  |  Methods in molecular biology (Clifton, N.J.)

High-throughput computational techniques have become invaluable tools to help increase the overall success, process efficiency, an..

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

Malancha Karmakar, James M Trauer, David B Ascher, Justin T Denholm

Journal article  |  2019  |  Journal of Infection

OBJECTIVES: The globally distributed "Beijing" lineage of Mycobacterium tuberculosis has been associated with outbreaks worldwide...

dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction

Lisa M Kaminskas, Douglas EV Pires, David B Ascher

Journal article  |  2019  |  Scientific Reports

Nanomedicine development currently suffers from a lack of efficient tools to predict pharmacokinetic behavior without relying upon..

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites

Maryia Karpiyevich, Sophie Adjalley, Marco Mol, David B Ascher, Bethany Mason, Gerbrand J van der Heden van Noort, Heike Laman, Huib Ovaa, Marcus CS Lee, Katerina Artavanis-Tsakonas

Journal article  |  2019  |  PLOS Pathogens

Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resista..

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

M Fleur Sernee, Julie E Ralton, Tracy L Nero, Lukasz F Sobala, Joachim Kloehn, Marcel A Vieira-Lara, Simon A Cobbold, Lauren Stanton, Douglas EV Pires, Eric Hanssen, Alexandra Males, Tom Ward, Laurence M Bastidas, Phillip L van der Peet, Michael W Parker, David B Ascher, Spencer J Williams, Gideon J Davies, Malcolm J McConville

Journal article  |  2019  |  Cell Host & Microbe

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

Vinayak Singh, Angela Pacitto, Stefano Donini, Davide M Ferraris, Sandor Boros, Eszter Illyes, Balint Szokol, Menico Rizzi, Tom L Blundell, David B Ascher, Janos Pato, Valerie Mizrahi

Journal article  |  2019  |  European Journal of Medicinal Chemistry

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

Xiaojing Sui, Douglas Pires, Shuai Nie, Giulia Vecchi, Michele Vendruscolo, David Ascher, Gavin Reid, Danny Hatters

Journal article  |  2019

SUMMARY The accumulation of wide range of different protein deposits in neurodegenerative diseases has been associated with the pr..

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

Carlos HM Rodrigues, Yoochan Myung, Douglas EV Pires, David B Ascher

Journal article  |  2019  |  Nucleic Acids Research

MTR-Viewer: identifying regions within genes under purifying selection

Michael Silk, Slave Petrovski, David B Ascher

Journal article  |  2019  |  Nucleic Acids Research

Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-caus..

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

David B Ascher, Ottavia Spiga, Martina Sekelska, Douglas EV Pires, Andrea Bernini, Monica Tiezzi, Jana Kralovicova, Ivana Borovska, Andrea Soltysova, Birgitta Olsson, Silvia Galderisi, Vittoria Cicaloni, Lakshminarayan Ranganath, Annalisa Santucci, Andrea Zatkova

Journal article  |  2019  |  European Journal of Human Genetics

Computational Saturation Mutagenesis to predict structural consequences of systematic mutations on protein stability and rifampin interactions in the β subunit of RNA polymerase in Mycobacterium leprae

Sundeep Chaitanya Vedithi, Carlos Rodrigues, Stephanie Portelli, Marcin Skwark, Madhusmita Das, David Ascher, Tom Blundell, Sony Malhotra

Journal article  |  2019

ABSTRACT In contrast to the situation with tuberculosis, rifampin resistance in leprosy may remain undetected due to the lack of r..

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

Malancha Karmakar, Carlos HM Rodrigues, Kathryn E Holt, Sarah J Dunstan, Justin Denholm, David B Ascher

Journal article  |  2019  |  PLOS ONE

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

Lisa M Kaminskas, Charlotte C Williams, Nathania J Leong, Linda J Chan, Neville J Butcher, Orlagh M Feeney, Christopher JH Porter, David Tyssen, Gilda Tachedjian, David B Ascher

Journal article  |  2019  |  European Journal of Pharmaceutics and Biopharmaceutics

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

Douglas EV Pires, Carlos HM Rodrigues, Amanda TS Albanaz, Malancha Karmakar, Yoochan Myung, Joicymara Xavier, Eleni-Maria Michanetzi, Stephanie Portelli, David B Ascher

Book Chapter  |  2019  |  Methods in Molecular Biology

The ability to predict how mutations affect protein structure, folding, and flexibility can elucidate the molecular mechanisms lea..

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

Journal article  |  2019  |  Journal of Medical Genetics

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

Stephanie Portelli, Jody E Phelan, David B Ascher, Taane G Clark, Nicholas Furnham

Journal article  |  2018  |  Scientific Reports

Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases

Palika Abayakoon, Yi Jin, James P Lingford, Marija Petricevic, Alan John, Eileen Ryan, Janice Wai-Ying Mui, Douglas E Pires, David B Ascher, Gideon J Davies, Ethan D Goddard-Borger, Spencer J Williams

Journal article  |  2018  |  ACS Central Science

Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy

Justin T Denholm, David B Ascher

Journal article  |  2018  |  American Journal of Respiratory and Critical Care Medicine

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

Carlos HM Rodrigues, Douglas E Pires, David B Ascher

Journal article  |  2018  |  Nucleic Acids Research

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

Carlos HM Rodrigues, David B Ascher, Douglas E Pires

Journal article  |  2018  |  Nucleic Acids Research

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

Kathryn E Holt, Paul McAdam, Vuong Khac Thai Phan, Thuy Thuong Thuong Nguyen, Thi Minh Ha Dang, Ngoc Lan Nguyen, Huu Lan Nguyen, Thi Quynh Nhu Nguyen, Thanh Hai Hoang, Thi Ngoc Ha Vu, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, et al.

Journal article  |  2018  |  Nature Genetics

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

Ales Hnizda, Milan Fabry, Takaya Moriyama, Petr Pachl, Michael Kugler, Vitezslav Brinsa, David B Ascher, William L Carroll, Petr Novak, Marketa Zaliova, Jan Trka, Pavlina Rezacova, Jun J Yang, Vaclav Veverka

Journal article  |  2018  |  Leukemia

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

Katrina A Andrews, David B Ascher, Douglas Eduardo Valente Pires, Daniel R Barnes, Lindsey Vialard, Ruth T Casey, Nicola Bradshaw, Julian Adlard, Simon Aylwin, Paul Brennan, Carole Brewer, Trevor Cole, Jackie A Cook, Rosemarie Davidson, Alan Donaldson, Alan Fryer, Lynn Greenhalgh, Shirley V Hodgson, Richard Irving, Fiona Lalloo, et al.

Journal article  |  2018  |  Journal of Medical Genetics

Fragment-Based Approach to Targeting Inosine-5 '-monophosphate Dehydrogenase (IMPDH) from &ITMycobacterium tuberculosis&IT

Ana Trapero, Angela Pacitto, Vinayak Singh, Mohamad Sabbah, Anthony G Coyne, Valerie Mizrahi, Tom L Blundell, David B Ascher, Chris Abell

Journal article  |  2018  |  Journal of Medicinal Chemistry

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

Sundeep Chaitanya Vedithi, Sony Malhotra, Madhusmita Das, Sheela Daniel, Nanda Kishore, Anuja George, Shantha Arumugam, Lakshmi Rajan, Mannam Ebenezer, David B Ascher, Eddy Arnold, Tom L Blundell

Journal article  |  2018  |  Scientific Reports

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt

Journal article  |  2018  |  Microbial Genomics

Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand.

Douglas EV Pires, Lisa M Kaminskas, David B Ascher

Journal article  |  2018  |  Methods in molecular biology (Clifton, N.J.)

A crucial factor for the approval and success of any drug is how it behaves in the body. Many drugs, however, do not reach the mar..

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Jane Hawkey, David Ascher, Louise Judd, Ryan Wick, Xenia Kostoulias, Heather Cleland, Denis Spelman, Alex Padiglione, Anton Peleg, Kathryn Holt

Journal article  |  2017

ABSTRACT Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in b..

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

Alfonso Trezza, Andrea Bernini, Andrea Langella, David B Ascher, Douglas EV Pires, Andrea Sodi, Ilaria Passerini, Elisabetta Pelo, Stanislao Rizzo, Neri Niccolai, Ottavia Spiga

Journal article  |  2017  |  Investigative Opthalmology & Visual Science

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

Joshua Traynelis, Michael Silk, Quanli Wang, Samuel F Berkovic, Liping Liu, David B Ascher, David J Balding, Slave Petrovski

Journal article  |  2017  |  Genome Research

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

Harry C Jubb, Arun P Pandurangan, Meghan A Turner, Bernardo Ochoa-Montano, Tom L Blundell, David B Ascher

Journal article  |  2017  |  Progress in Biophysics and Molecular Biology

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

Douglas EV Pires, David B Ascher

Journal article  |  2017  |  Nucleic Acids Research

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

Arun Prasad Pandurangan, Bernardo Ochoa-Montano, David B Ascher, Tom L Blundell

Journal article  |  2017  |  Nucleic Acids Research

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

Amanda TS Albanaz, Carlos HM Rodrigues, Douglas EV Pires, David B Ascher

Journal article  |  2017  |  Expert Opinion on Drug Discovery

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

Yasmin M Ramdzan, Mikhail M Trubetskov, Angelique R Ormsby, Estella A Newcombe, Xiaojing Sui, Mark J Tobin, Marie N Bongiovanni, Sally L Gras, Grant Dewson, Jason ML Miller, Steven Finkbeiner, Nagaraj S Moily, Jonathan Niclis, Clare L Parish, Anthony W Purcell, Michael J Baker, Jacqueline A Wilce, Saboora Waris, Diana Stojanovski, Till Bocking, et al.

Journal article  |  2017  |  Cell reports

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

Ruth T Casey, David B Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A Andrews, Helen L Simpson, Benjamen Challis, Soo-Mi Park, Venkata R Bulusu, Fiona Lalloo, Douglas EV Pires, Hannah West, Graeme R Clark, Philip S Smith, James Whitworth, Thomas G Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D Hurst, Emma R Woodward, et al.

Journal article  |  2017  |  Molecular Genetics & Genomic Medicine

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

Julie A Sharp, Amelia J Brennan, Galina Polekhina, David B Ascher, Christophe Lefevre, Kevin R Nicholas

Journal article  |  2017  |  Cellular Signalling

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

Arun Prasad Pandurangan, David B Ascher, Sherine E Thomas, Tom L Blundell

Journal article  |  2017  |  Biochemical Society Transactions

Familial STAG2 germline mutation defines a new human cohesinopathy

Fernanda C Soardi, Alice Machado-Silva, Natalia D Linhares, Ge Zheng, Qianhui Qu, Heloisa B Pena, Thaia MM Martins, Helaine GS Vieira, Nubia B Pereira, Raquel C Melo-Minardi, Carolina C Gomes, Ricardo S Gomez, Dawidson A Gomes, Douglas EV Pires, David B Ascher, Hongtao Yu, Sergio DJ Pena

Journal article  |  2017  |  npj Genomic Medicine

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

Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montano, Will R Pitt, David B Ascher, Tom L Blundell

Journal article  |  2017  |  Journal of Molecular Biology

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

Bancinyane L Sibanda, Dimitri Y Chirgadze, David B Ascher, Tom L Blundell

Journal article  |  2017  |  Science

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

Lorien J Parker, Alessio Bocedi, David B Ascher, Jade B Aitken, Hugh H Harris, Mario Lo Bello, Giorgio Ricci, Craig J Morton, Michael W Parker

Journal article  |  2017  |  Protein Science

Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached

S Liang, SR Esswein, T Ochi, Q Wu, DB Ascher, D Chirgadze, BL Sibanda, TL Blundell

Journal article  |  2017  |  Structural Chemistry

Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis

Yumi Park, Angela Pacitto, Tracy Bayliss, Laura AT Cleghorn, Zhe Wang, Travis Hartman, Kriti Arora, Thomas R Ioerger, Jim Sacchettini, Menico Rizzi, Stefano Donini, Tom L Blundell, David B Ascher, Kyu Rhee, Ardala Breda, Nian Zhou, Veronique Dartois, Surendranadha Reddy Jonnala, Laura E Via, Valerie Mizrahi, et al.

Journal article  |  2017  |  ACS Infectious Diseases

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

Dimitri Y Chirgadze, David B Ascher, Tom L Blundell, Bancinyane L Sibanda

Journal article  |  2017  |  Methods in enzymology

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

Vinayak Singh, Stefano Donini, Angela Pacitto, Claudia Sala, Ruben C Hartkoorn, Neeraj Dhar, Gyorgy Keri, David B Ascher, Guillaume Mondesert, Anthony Vocat, Andreanne Lupien, Raphael Sommer, Helene Vermet, Sophie Lagrane, Joe Buechler, Digby F Warner, John D McKinney, Janos Pato, Stewart T Cole, Tom L Blundell, et al.

Journal article  |  2017  |  ACS Infectious Diseases

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

Flora S Kano, Flavia A Souza-Silva, Leticia M Torres, Barbara AS Lima, Tais N Sousa, Jessica RS Alves, Roberto S Rocha, Cor JF Fontes, Bruno AM Sanchez, John H Adams, Cristiana FA Brito, Douglas EV Pires, David B Ascher, Ana Maria Sell, Luzia H Carvalho

Journal article  |  2016  |  PLOS Neglected Tropical Diseases

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

Rhiannon R White, Amy H Ponsford, Michael P Weekes, Rachel B Rodrigues, David B Ascher, Marco Mol, Murray E Selkirk, Steven P Gygi, Christopher M Sanderson, Katerina Artavanis-Tsakonas

Journal article  |  2016  |  PLOS Pathogens

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

Miguel B Coelho, David B Ascher, Clare Gooding, Emma Lang, Hannah Maude, David Turner, Miriam Llorian, Douglas EV Pires, Jan Attig, Christopher WJ Smith

Journal article  |  2016  |  Biochemical Society Transactions

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

Ana Carolina Rios Silvino, Gabriel Luiz Costa, Flavia Carolina Faustino de Araujo, David Benjamin Ascher, Douglas Eduardo Valente Pires, Cor Jesus Fernandes Fontes, Luzia Helena Carvalho, Cristiana Ferreira Alves de Brito, Tais Nobrega Sousa

Journal article  |  2016  |  PLOS ONE

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

Douglas EV Pires, David B Ascher

Journal article  |  2016  |  Nucleic Acids Research

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

Douglas EV Pires, David B Ascher

Journal article  |  2016  |  Nucleic Acids Research

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

Douglas EV Pires, Tom L Blundell, David B Ascher

Journal article  |  2016  |  Scientific Reports

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

Linda J Chan, David B Ascher, Rajbharan Yadav, Juergen B Bulitta, Charlotte C Williams, Christopher JH Porter, Cornelia B Landersdorfer, Lisa M Kaminskas

Journal article  |  2016  |  Molecular Pharmaceutics

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

Jody Phelan, Francesc Coll, Ruth McNerney, David B Ascher, Douglas EV Pires, Nick Furnham, Nele Coeck, Grant A Hill-Cawthorne, Mridul B Nair, Kim Mallard, Andrew Ramsay, Susana Campino, Martin L Hibberd, Arnab Pain, Leen Rigouts, Taane G Clark

Journal article  |  2016  |  BMC Medicine

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

Douglas EV Pires, Jing Chen, Tom L Blundell, David B Ascher

Journal article  |  2016  |  Scientific Reports

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

Martina Nemethova, Jan Radvanszky, Ludevit Kadasi, David B Ascher, Douglas EV Pires, Tom L Blundell, Berardino Porfirio, Alessandro Mannoni, Annalisa Santucci, Lia Milucci, Silvia Sestini, Gianfranco Biolcati, Fiammetta Sorge, Caterina Aurizi, Robert Aquaron, Mohammed Alsbou, Charles Marques Lourenco, Kanakasabapathi Ramadevi, Lakshminarayan R Ranganath, James A Gallagher, et al.

Journal article  |  2016  |  European Journal of Human Genetics

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

Angela Pacitto, David B Ascher, Louise H Wong, Beata K Blaszczyk, Ravi K Nookala, Nianshu Zhang, Svetlana Dokudovskaya, Tim P Levine, Tom L Blundell

Journal article  |  2015  |  Open Biology

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

Harry Jubb, Tom L Blundell, David B Ascher

Journal article  |  2015  |  Progress in Biophysics and Molecular Biology

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

Michal Blaszczyk, Nicholas J Harmer, Dimitri Y Chirgadze, David B Ascher, Tom L Blundell

Journal article  |  2015  |  Progress in Biophysics and Molecular Biology

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

Mariam Jafri, Naomi C Wake, David B Ascher, Douglas EV Pires, Dean Gentle, Mark R Morris, Eleanor Rattenberry, Michael A Simpson, Richard C Trembath, Astrid Weber, Emma R Woodward, Alan Donaldson, Tom L Blundell, Farida Latif, Eamonn R Maher

Journal article  |  2015  |  Cancer Discovery

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

Douglas EV Pires, Tom L Blundell, David B Ascher

Journal article  |  2015  |  Journal of Medicinal Chemistry

PEGylated Interferon Displays Differences in Plasma Clearance and Bioavailability Between Male and Female Mice and Between Female Immunocompetent C57Bl/6J and Athymic Nude Mice

Cornelia B Landersdorfer, Suzanne M Caliph, David M Shackleford, David B Ascher, Lisa M Kaminskas

Journal article  |  2015  |  Journal of Pharmaceutical Sciences

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

Linda J Chan, Juergen B Bulitta, David B Ascher, John M Haynes, Victoria M McLeod, Christopher JH Porter, Charlotte C Williams, Lisa M Kaminskas

Journal article  |  2015  |  Molecular Pharmaceutics

Practical Lessons in Murine Thoracic Lymph Duct Cannulations: Observations in Female and Male Mice Across Four Different Strains That Impact on "Cannulatability"

Suzanne M Caliph, David M Shackleford, David B Ascher, Lisa M Kaminskas

Journal article  |  2015  |  Journal of Pharmaceutical Sciences

Methotrexate-Conjugated PEGylated Dendrimers Show Differential Patterns of Deposition and Activity in Tumor-Burdened Lymph Nodes after Intravenous and Subcutaneous Administration in Rats

Lisa M Kaminskas, Victoria M McLeod, David B Ascher, Gemma M Ryan, Seth Jones, John M Haynes, Natalie L Trevaskis, Linda J Chan, Erica K Sloan, Bentamin A Finnin, Mark Williamson, Tony Velkov, Elizabeth D Williams, Brian D Kelly, David J Owen, Christopher JH Porter

Journal article  |  2015  |  Molecular Pharmaceutics

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

Stefan J Hermans, David B Ascher, Nancy C Hancock, Jessica K Holien, Belinda J Michell, Siew Yeen Chai, Craig J Morton, Michael W Parker

Journal article  |  2015  |  Protein Science

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

Douglas EV Pires, Tom L Blundell, David B Ascher

Journal article  |  2015  |  Nucleic Acids Research

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

Jeannette L Usher, David B Ascher, Douglas EV Pires, Anna M Milan, Tom L Blundell, Lakshminarayan R Ranganath

Journal article  |  2015  |  JIMD reports

Protein-protein interactions: Structures and druggability

DB Ascher, HC Jubb, DEV Pires, T Ochi, A Higueruelo, TL Blundell

Book Chapter  |  2015

Protein-Protein Interactions: Structures and Druggability

David B Ascher, Harry C Jubb, Douglas EV Pires, Takashi Ochi, Alicia Higueruelo, Tom L Blundell

Journal article  |  2015  |  Multifaceted Roles of Crystallography in Modern Drug Discovery

Exploring the chemical space of the lysine-binding pocket of the first kringle domain of hepatocyte growth factor/scatter factor (HGF/SF) yields a new class of inhibitors of HGF/SF-MET binding

AG Sigurdardottir, A Winter, A Sobkowicz, M Fragai, D Chirgadze, DB Ascher, TL Blundell, E Gherardi

Journal article  |  2015  |  Chemical Science

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

Andrew D Watt, Gabriela AN Crespi, Russell A Down, David B Ascher, Adam Gunn, Keyla A Perez, Catriona A McLean, Victor L Villemagne, Michael W Parker, Kevin J Barnham, Luke A Miles

Journal article  |  2014  |  Acta Neuropathologica

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

Douglas EV Pires, David B Ascher, Tom L Blundell

Journal article  |  2014  |  Nucleic Acids Research

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

Andrew D Watt, Gabriela AN Crespi, Russell A Down, David B Ascher, Adam Gunn, Keyla A Perez, Catriona A McLean, Victor L Villemagne, Michael W Parker, Kevin J Barnham, Luke A Miles

Journal article  |  2014  |  Acta Neuropathologica

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

David B Ascher, Jerome Wielens, Tracy L Nero, Larissa Doughty, Craig J Morton, Michael W Parker

Journal article  |  2014  |  Scientific Reports

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

Gabriela AN Crespi, David B Ascher, Michael W Parker, Luke A Miles

Journal article  |  2014  |  Acta Crystallographica Section F Structural Biology Communications

Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration

Susanne C Feil, David B Ascher, Michael J Kuiper, Rodney K Tweten, Michael W Parker

Journal article  |  2014  |  Journal of Molecular Biology

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

Douglas EV Pires, David B Ascher, Tom L Blundell

Journal article  |  2014  |  Bioinformatics

PEGylation of interferon alpha 2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases

Lisa M Kaminskas, David B Ascher, Victoria M McLeod, Marco J Herold, Caroline P Le, Erica K Sloan, Christopher JH Porter

Journal article  |  2013  |  Journal of Controlled Release

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

Galina Polekhina, David Benjamin Ascher, Shie Foong Kok, Simone Beckham, Matthew Wilce, Mark Waltham

Journal article  |  2013  |  Acta Crystallographica Section D Biological Crystallography

Structural approaches to probing metal interaction with proteins

Lorien J Parker, David B Ascher, Chen Gao, Luke A Miles, Hugh H Harris, Michael W Parker

Journal article  |  2012  |  Journal of Inorganic Biochemistry

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

David B Ascher, Galina Polekhina, Michael W Parker

Journal article  |  2012  |  Acta Crystallographica Section F - Structural Biology and Crystallization Communications

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

Lorien J Parker, Louis C Italiano, Craig J Morton, Nancy C Hancock, David B Ascher, Jade B Aitken, Hugh H Harris, Pablo Campomanes, Ursula Rothlisberger, Anastasia De Luca, Mario Lo Bello, Wee Han Ang, Paul J Dyson, Michael W Parker

Journal article  |  2011  |  Chemistry - A European Journal

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

Galina Polekhina, David Benjamin Ascher, Shie Foong Kok, Mark Waltham

Journal article  |  2011  |  Acta Crystallographica Section F Structural Biology and Crystallization Communications

Regulation of Insulin-Regulated Membrane Aminopeptidase Activity by Its C-Terminal Domain

David B Ascher, Brett A Cromer, Craig J Morton, Irene Volitakis, Robert A Cherny, Anthony L Albiston, Siew Yeen Chai, Michael W Parker

Journal article  |  2011  |  Biochemistry

Novel Therapeutic Approaches to Treat Alzheimer’s Disease and Memory Disorders

David B Ascher, Gabriela AN Crespi, Hooi Ling Ng, Craig J Morton, Michael W Parker, Luke A Miles

Journal article  |  2008  |  Journal of Proteomics & Bioinformatics

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

Siew Yeen Chai, Holly R Yeatman, Michael W Parker, David B Ascher, Philip E Thompson, Hayley T Mulvey, Anthony L Albiston

Journal article  |  2008  |  BMC Neuroscience

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

Anthony L Albiston, Craig J Morton, Hooi Ling Ng, Vi Pham, Holly R Yeatman, Siying Ye, Ruani N Fernando, Dimitri De Bundel, David B Ascher, Frederick AO Mendelsohn, Michael W Parker, Siew Yeen Chai

Journal article  |  2008  |  FASEB Journal

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

Siying Ye, Siew Yeen Chai, Rebecca A Lew, David B Ascher, Craig J Morton, Michael W Parker, Anthony L Albiston

Journal article  |  2008  |  International Journal of Biochemistry and Cell Biology

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

Kwok S Wun, Luke A Miles, Gabriela AN Crespi, Kaye Wycherley, David B Ascher, Kevin J Barnham, Roberto Cappai, Konrad Beyreuther, Colin L Masters, Michael W Parker, William J McKinstry

Journal article  |  2008  |  Acta Crystallographica Section F - Structural Biology and Crystallization Communications