D. Pires

发表

An integrated computational approach can classify VHL missense mutations according to risk of clear cell renal carcinoma

T. Blundell, M. Bycroft, Á. Olivera-Nappa, 2014, Human molecular genetics.

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

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2019, Nucleic Acids Res..

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2016, Scientific Reports.

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

Richard C Trembath, Alan Donaldson, Tom L Blundell, 2015, Cancer discovery.

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

M. Vendruscolo, G. Reid, D. Ascher, 2019, bioRxiv.

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

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2020, Nucleic Acids Res..

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

M. Vendruscolo, G. Reid, D. Ascher, 2020, Proceedings of the National Academy of Sciences.

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

Carlos H. M. Rodrigues, Joicymara S. Xavier, D. Ascher, 2019, Methods in molecular biology.

Phillipe Taniere, Louise Izatt, Douglas E V Pires, 2017, Molecular genetics & genomic medicine.

Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases

Spencer J. Williams, G. Davies, D. Ascher, 2018, ACS central science.

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

Nicholas Furnham, D. Ascher, D. Pires, 2020, Scientific Reports.

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

D. Ascher, Lipi Thukral, D. Pires, 2020, Autophagy.

COVID-3D: An online resource to explore the structural distribution of genetic variation in SARS-CoV-2 and its implication on therapeutic development

Carlos H. M. Rodrigues, D. Ascher, M. Olshansky, 2020, bioRxiv.

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

D. Ascher, D. Pires, Yoochan Myung, 2020, Nucleic Acids Res..

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

Carlos H. M. Rodrigues, D. Ascher, M. Olshansky, 2020, Nature genetics.

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

Spencer J. Williams, T. Nero, M. Parker, 2019, Cell host & microbe.

A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism

I. Helbig, B. Kennedy, A. Gelot, 2022, bioRxiv.

cropCSM: designing safe and potent herbicides with graph-based signatures

D. Ascher, J. Mylne, K. Stubbs, 2022, Briefings Bioinform..

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures

Qisheng Pan, D. Ascher, D. Pires, 2022, Briefings Bioinform..

Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2

D. Ascher, D. Pires, Mengyuan Shen, 2022, Scientific Reports.

Evaluating hierarchical machine learning approaches to classify biological databases

Pâmela M. Rezende, Joicymara S. Xavier, D. Ascher, 2022, Briefings Bioinform..

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

Douglas E. V. Pires, C. Gooding, C. Smith, 2016, Biochemical Society transactions.

A microbial sulfoquinovose monooxygenase pathway that enables sulfosugar assimilation

Nichollas E. Scott, Eleanor C. Saunders, Spencer J. Williams, 2021 .

kinCSM: Using graph‐based signatures to predict small molecule CDK2 inhibitors

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2022, Protein science : a publication of the Protein Society.

Identifying the molecular drivers of ALS-implicated missense mutations

D. Ascher, D. Pires, Stephanie Portelli, 2022, Journal of Medical Genetics.

cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules

João P. L. Velloso, D. Ascher, D. Pires, 2022, J. Chem. Inf. Model..

Structural landscapes of PPI interfaces

Carlos H. M. Rodrigues, T. Blundell, D. Ascher, 2022, Briefings Bioinform..

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2015, Journal of medicinal chemistry.

Searching for plant-derived antivirals against dengue virus and Zika virus

Douglas E. V. Pires, E. Kroon, L. Rosa, 2022, Virology journal.

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

D. Ascher, L. H. Carvalho, D. Pires, 2018, PloS one.

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

D. Ascher, L. H. Carvalho, D. Pires, 2016, PloS one.

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2016, Scientific Reports.

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2014, Nucleic Acids Res..

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

Carlos H M Rodrigues, David B Ascher, Yoochan Myung, 2019, Bioinform..

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

Carlos H M Rodrigues, Douglas E V Pires, David B Ascher, 2017, Expert opinion on drug discovery.

A structural biology community assessment of AlphaFold2 applications

Douglas E. V. Pires, Norman E. Davey, Carlos H. M. Rodrigues, 2021, bioRxiv.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr

M. Carvalho, M. A. Machado, M. D. da Silva, 2021, Tropical Animal Health and Production.

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2014, Nucleic Acids Res..

The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assay.

D. Ascher, D. Pires, R. Monte-Neto, 2021, Biochimica et biophysica acta. Biomembranes.

Repurposed Molecules: A New Hope in Tackling Neglected Infectious Diseases

Douglas E. V. Pires, Christopher Fernandez-Prada, Noelie Douanne, 2019, In Silico Drug Design.

Protein-Protein Interactions: Structures and Druggability

Alicia P. Higueruelo, T. Blundell, H. Jubb, 2015 .

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

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2021, Computational and structural biotechnology journal.

Familial STAG2 germline mutation defines a new human cohesinopathy

Q. Qu, Hongtao Yu, D. Ascher, 2017, npj Genomic Medicine.

Familial STAG2 germline mutation defines a new human cohesinopathy

Hongtao Yu, Douglas E V Pires, David B Ascher, 2017, npj Genomic Medicine.

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

Douglas E. V. Pires, David B. Ascher, D. Ascher, 2016, Nucleic Acids Res..

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

Douglas E. V. Pires, David B. Ascher, D. Ascher, 2016, Nucleic Acids Res..

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

Douglas E. V. Pires, Francesc Coll, Ruth McNerney, 2016, BMC Medicine.

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

Ludevit Kadasi, Jan Radvanszky, Andrea Zatkova, 2015, European Journal of Human Genetics.

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2015, JIMD reports.

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

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher, 2013, Bioinform..

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

Andrea Bernini, Andrea Sodi, Ottavia Spiga, 2017, Investigative ophthalmology & visual science.

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

Douglas E. V. Pires, David B. Ascher, John H. Adams, 2016, PLoS neglected tropical diseases.

epitope3D: a machine learning method for conformational B-cell epitope prediction

D. Ascher, D. Pires, Yoochan Myung, 2021, Briefings Bioinform..

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

Douglas E. V. Pires, David B. Ascher, Carlos H. M. Rodrigues, 2018, Nucleic Acids Res..

mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions

Douglas E. V. Pires, Carlos H. M. Rodrigues, D. Ascher, 2021, Nucleic Acids Res..

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

Douglas E. V. Pires, Soo-Mi Park, A. Antoniou, 2018, Journal of Medical Genetics.

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

P. Devilee, H. Neumann, D. Ascher, 2019, Journal of Medical Genetics.

Tumour risks and genotype–phenotype–proteotype analysis of patients with germline mutations in the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD

D. Goudie, N. Bradshaw, F. Lalloo, 2016, The Lancet.

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

Douglas E. V. Pires, R. Coimbra, D. Ascher, 2021, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

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

J. Královičová, D. Ascher, L. Ranganath, 2019, European Journal of Human Genetics.

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

Douglas E. V. Pires, Carlos H M Rodrigues, Douglas E V Pires, 2020, Protein science : a publication of the Protein Society.

Germline Mutations in the CDKN 2 B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma

T. Blundell, M. Simpson, R. Trembath, 2015 .

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

Lisa M Kaminskas, Douglas E V Pires, David B Ascher, 2018, Methods in molecular biology.

ThermoMutDB: a thermodynamic database for missense mutations

Douglas E. V. Pires, Stephanie Portelli, David B. Ascher, 2020, Nucleic Acids Res..

Distinguishing between PTEN clinical phenotypes through mutation analysis

D. Ascher, Lucy Barr, D. Pires, 2021, Computational and structural biotechnology journal.

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis

Edward Airey, Stephanie Portelli, Joicymara S Xavier, 2021, Artificial Neural Networks, 3rd Edition.

mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria

David B Ascher, Douglas Pires, D. Ascher, 2020, J. Chem. Inf. Model..

CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function

D. Ascher, D. Pires, Yoochan Myung, 2021, Bioinform..

Evolution of a New Pathway of Reserve Carbohydrate Biosynthesis in Leishmania Parasites

Spencer J. Williams, T. Nero, M. Parker, 2019, SSRN Electronic Journal.

MTR3D: identifying regions within protein tertiary structures under purifying selection

Douglas E. V. Pires, Carlos H. M. Rodrigues, N. Thorne, 2021, Nucleic Acids Res..

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

Stephanie Portelli, Joicymara S Xavier, Michael Silk, 2020, Methods in molecular biology.

pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties

Douglas E. V. Pires, Raghad Al-Jarf, David B. Ascher, 2021, J. Chem. Inf. Model..

dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction

David B Ascher, Lisa M Kaminskas, Douglas E V Pires, 2019, Scientific Reports.

CSM‐peptides: A computational approach to rapid identification of therapeutic peptides

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2022, Protein Science.

TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction

D. Ascher, D. Pires, A. Alavi, 2021, Molecular therapy. Nucleic acids.

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors

Douglas E. V. Pires, David B. Ascher, Carlos H. M. Rodrigues, 2021, J. Chem. Inf. Model..

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

Douglas E. V. Pires, David B. Ascher, Carlos H. M. Rodrigues, 2018, Nucleic Acids Res..

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

David B. Ascher, Douglas E.V. Pires, D. Ascher, 2017, Nucleic Acids Res..

embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules

D. Ascher, D. Pires, R. Al-Jarf, 2023, J. Chem. Inf. Model..

toxCSM: comprehensive prediction of small molecule toxicity profiles

D. Ascher, D. Pires, Stephanie Portelli, 2022, Briefings Bioinform..

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

Michael Silk, Carlos H. Silveira, Yoochan Myung, 2020, Bioinform..

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

Douglas E. V. Pires, D. Ascher, L. H. Carvalho, 2016, PloS one.

mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity

D. Ascher, D. Pires, Yoochan Myung, 2021, NAR genomics and bioinformatics.

University of Birmingham SDHA related tumorigenesis:

Soo-Mi Park, Rosina Savisaar, F. Lalloo, 2017 .

University of Birmingham SDHA related tumorigenesis:

Soo-Mi Park, Rosina Savisaar, F. Lalloo, 2017 .

SARS-CoV-2 Africa dashboard for real-time COVID-19 information

Joicymara S. Xavier, T. de Oliveira, D. Ascher, 2022, Nature Microbiology.

AI driven B-cell Immunotherapy Design

D. Ascher, D. Pires, B. M. D. Silva, 2023, ArXiv.

DDMut: predicting effects of mutations on protein stability using deep learning

Carlos H. M. Rodrigues, Qisheng Pan, D. Ascher, 2023, Nucleic Acids Res..

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

J. Královičová, D. Ascher, L. Ranganath, 2019, European Journal of Human Genetics.

LEGO-CSM: a tool for functional characterization of proteins

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2023, Bioinformatics.

Understanding the complementarity and plasticity of antibody–antigen interfaces

D. Ascher, D. Pires, Yoochan Myung, 2023, Bioinformatics.

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

Carlos H. M. Rodrigues, D. Ascher, D. Pires, 2017, Expert Opinion on Drug Discovery.

An integrated computational approach can classify VHL missense mutations according to risk of clear cell renal carcinoma

T. Blundell, M. Bycroft, Á. Olivera-Nappa, 2014, Human molecular genetics.

Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT pdf

Karin M. Verspoor, Karin Verspoor, Aparna Elangovan, 2021, BMC Bioinform..

epitope1D: accurate taxonomy-aware B-cell linear epitope prediction

D. Ascher, D. Pires, B. D. da Silva, 2022, bioRxiv.

AI-driven GPCR analysis, engineering, and targeting.

João P. L. Velloso, D. Ascher, D. Pires, 2024, Current opinion in pharmacology.