Douglas Pires

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

Yoochan Myung, Douglas EV Pires, David B Ascher

Journal article  |  2020  |  Nucleic Acids Research

While antibodies are becoming an increasingly important therapeutic class, especially in personalized medicine, their development ..

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

Douglas EV Pires, Wandré NP Veloso, YooChan Myung, Carlos HM Rodrigues, Michael Silk, Pâmela M Rezende, Francislon Silva, Joicymara S Xavier, João PL Velloso, Carlos H da Silveira, David B Ascher

Journal article  |  2020  |  Bioinformatics

SUMMARY: EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive inte..

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..

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 ..

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 ..

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..

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..

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

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

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

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..

Repurposed Molecules: A New Hope in Tackling Neglected Infectious Diseases

C Fernández-Prada, N Douanne, A Minguez-Menendez, J Pena, LG Tunes, DEV Pires, RL Monte-Neto

Book Chapter  |  2019

Neglected infectious diseases (NIDs) are a group of chronic, debilitating, and poverty-promoting diseases, which include parasitic..

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

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

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

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..

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

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

Douglas EV Pires, David B Ascher

Journal article  |  2017  |  Nucleic Acids Research

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms

Joao PA Moraes, Gisele L Pappa, Douglas EV Pires, Sandro C Izidoro

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

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

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

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

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

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

PDBest: a user-friendly platform for manipulating and enhancing protein structures

Wellisson RS Goncalves, Valdete M Goncalves-Almeida, Aleksander L Arruda, Wagner Meira, Carlos H da Silveira, Douglas EV Pires, Raquel C de Melo-Minardi

Journal article  |  2015  |  Bioinformatics

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

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

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

Lucy Gossage, Douglas EV Pires, Alvaro Olivera-Nappa, Juan Asenjo, Mark Bycroft, Tom L Blundell, Tim Eisen

Journal article  |  2014  |  Human Molecular Genetics

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

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

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

Douglas EV Pires, Raquel C de Melo-Minardi, Carlos H da Silveira, Frederico F Campos, Wagner Meira

Journal article  |  2013  |  Bioinformatics

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids

VM Goncalves-Almeida, DEV Pires, RC de Melo-Minardi, CH da Silveira, W Meira, MM Santoro

Journal article  |  2012  |  Bioinformatics

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

Douglas EV Pires, Raquel C de Melo-Minardi, Marcos A dos Santos, Carlos H da Silveira, Marcelo M Santoro, Wagner Meira

Journal article  |  2011  |  BMC Genomics

Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins

Carlos H da Silveira, Douglas EV Pires, Raquel C Minardi, Cristina Ribeiro, Caio JM Veloso, Julio CD Lopes, Wagner Meira, Goran Neshich, Carlos HI Ramos, Raul Habesch, Marcelo M Santoro

Journal article  |  2009  |  Proteins: Structure, Function, and Bioinformatics

A campaign-based characterization of spamming strategies

PH Calais, DEV Pires, DO Guedes, W Meira, C Hoepers, K Steding-Jessen

Conference Proceedings  |  2008  |  5th Conference on Email and Anti-Spam, CEAS 2008