Douglas Pires

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis.

Edward Airey, Stephanie Portelli, Joicymara S Xavier, Yoo Chan Myung, Michael Silk, Malancha Karmakar, João PL Velloso, Carlos HM Rodrigues, Hardik H Parate, Anjali Garg, Raghad Al-Jarf, Lucy Barr, Juliana A Geraldo, Pâmela M Rezende, Douglas EV Pires, David B Ascher

Journal article  |  2021  |  Methods in molecular biology (Clifton, N.J.)

Mutations in protein-coding regions can lead to large biological changes and are associated with genetic conditions, including can..

ThermoMutDB: a thermodynamic database for missense mutations.

Joicymara S Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M Rezende, João PL Velloso, David B Ascher, Douglas EV Pires

Journal article  |  2020  |  Nucleic Acids Research

Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on their fol..

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

Stephanie Portelli, Yoochan Myung, Nicholas Furnham, Sundeep Chaitanya Vedithi, Douglas EV Pires, David B Ascher

Journal article  |  2020  |  Scientific Reports

Rifampicin resistance is a major therapeutic challenge, particularly in tuberculosis, leprosy, P. aeruginosa and S. aureus infecti..

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

Carlos HM Rodrigues, Douglas EV Pires, David B Ascher

Journal article  |  2020  |  Protein Science

Predicting the effect of missense variations on protein stability and dynamics is important for understanding their role in diseas..

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

Stephanie Portelli, Moshe Olshansky, Carlos HM Rodrigues, Elston N D'Souza, Yoochan Myung, Michael Silk, Azadeh Alavi, Douglas E Pires, David B Ascher

Journal article  |  2020  |  Nature Genetics

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..

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

Douglas E Pires, David B Ascher

Journal article  |  2020  |  Journal of Chemical Information and Modeling

Development of new potent, safe drugs to treat Mycobacteria has proven to be challenging, with limited hit rates of initial screen..

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

Yoochan Myung, Douglas E 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 ..

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

Douglas EV Pires, Carlos HM Rodrigues, David B Ascher

Journal article  |  2020  |  Nucleic Acids Research

Significant efforts have been invested into understanding and predicting the molecular consequences of mutations in protein coding..

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..