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

Application of next generation sequencing for the detection of human viral pathogens in clinical specimens

(2017) Jayme Parker et al.   JOURNAL OF CLINICAL VIROLOGY

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

(2017) Harry C Jubb et al.   JOURNAL OF MOLECULAR BIOLOGY

The allosteric inhibitor ABL001 enables dual targeting of BCR–ABL1

(2017) Andrew A. Wylie et al.   NATURE

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

(2017) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Harry C. Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

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

(2017) Bancinyane L. Sibanda et al.   SCIENCE

Familial STAG2 germline mutation defines a new human cohesinopathy

(2017) Fernanda C. Soardi et al.   npj Genomic Medicine

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

(2017) Ruth T. Casey et al.   Molecular Genetics & Genomic Medicine

Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2014–2015

(2016) Aeron C. Hurt et al.   ANTIVIRAL RESEARCH

Binding of Clinical Inhibitors to a Model Precursor of a Rationally Selected Multidrug Resistant HIV-1 Protease Is Significantly Weaker Than That to the Released Mature Enzyme

(2016) Joon H. Park et al.   BIOCHEMISTRY

ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity

(2016) Daniel K. Witvliet et al.   BIOINFORMATICS

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

MAESTROweb: a web server for structure-based protein stability prediction

(2016) Josef Laimer et al.   BIOINFORMATICS

Structure-based discovery of novel 4,5,6-trisubstituted pyrimidines as potent covalent Bruton’s tyrosine kinase inhibitors

(2016) Yi Zou et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

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

(2016) Jody Phelan et al.   BMC Medicine

Drug Resistance to EGFR Inhibitors in Lung Cancer

(2016) Osamu Tetsu et al.   CHEMOTHERAPY

Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor

(2016) Guodong Hu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Computational Prediction of HIV-1 Resistance to Protease Inhibitors

(2016) Ali Hosseini et al.   Journal of Chemical Information and Modeling

Resistance to Mutant Group 2 Influenza Virus Neuraminidases of an Oseltamivir-Zanamivir Hybrid Inhibitor

(2016) Yan Wu et al.   JOURNAL OF VIROLOGY

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

(2016) Katrina A Andrews et al.   LANCET

Rethink the links between genes and disease

(2016)   NATURE

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

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

(2016) Minghui Li et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Ana Carolina Rios Silvino et al.   PLoS One

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

(2016) S. Liang et al.   STRUCTURAL CHEMISTRY

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

(2016) Douglas E. V. Pires et al.   Scientific Reports

Current and novel antiviral strategies for influenza infection

(2016) Hui-Ling Yen   Current Opinion in Virology

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

(2016) Flora S. Kano et al.   PLoS Neglected Tropical Diseases

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

(2016) Rhiannon R. White et al.   PLoS Pathogens

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

(2016) Vinayak Singh et al.   ACS Infectious Diseases

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

(2016) Yumi Park et al.   ACS Infectious Diseases

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

(2016) Douglas E. V. Pires et al.   Scientific Reports

Neuraminidase mutations conferring resistance to laninamivir lead to faster drug binding and dissociation

(2015) Jennifer L. McKimm-Breschkin et al.   ANTIVIRAL RESEARCH

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

(2015) Martina Nemethova et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

(2015) Douglas E. V. Pires et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ins and outs of selective kinase inhibitor development

(2015) Susanne Müller et al.   Nature Chemical Biology

Kinase inhibitors and monoclonal antibodies in oncology: clinical implications

(2015) Helen Gharwan et al.   Nature Reviews Clinical Oncology

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

(2015) Vincent Frappier et al.   NUCLEIC ACIDS RESEARCH

Allosteric small-molecule kinase inhibitors

(2015) Peng Wu et al.   PHARMACOLOGY & THERAPEUTICS

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

(2015) Michal Blaszczyk et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

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

(2015) A. G. Sigurdardottir et al.   Chemical Science

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

(2015) M. Jafri et al.   Cancer Discovery

Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012–2013

(2014) Adam Meijer et al.   ANTIVIRAL RESEARCH

Type III or allosteric kinase inhibitors for the treatment of non-small cell lung cancer

(2014) Morena Fasano et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases

(2014) Sandra W Cowan-Jacob et al.   Future Medicinal Chemistry

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

(2014) Lucy Gossage et al.   HUMAN MOLECULAR GENETICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Genetic testing in the epilepsies—developments and dilemmas

(2014) Annapurna Poduri et al.   Nature Reviews Neurology

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

(2014) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors

(2014) Li Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Stefan J. Hermans et al.   PROTEIN SCIENCE

Safety and efficacy of peramivir for influenza treatment

(2014) Atsuko Hata et al.   Drug Design Development and Therapy

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

(2014) David B. Ascher et al.   Scientific Reports

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

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

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

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Novel P2 Tris-tetrahydrofuran Group in Antiviral Compound 1 (GRL-0519) Fills the S2 Binding Pocket of Selected Mutants of HIV-1 Protease

(2013) Hongmei Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Structural basis for a class of nanomolar influenza A neuraminidase inhibitors

(2013) Philip S. Kerry et al.   Scientific Reports

Influenza neuraminidase inhibitors: antiviral action and mechanisms of resistance

(2012) Jennifer L. McKimm-Breschkin   Influenza and Other Respiratory Viruses

Combinatorial Effect of Two Framework Mutations (E119V and I222L) in the Neuraminidase Active Site of H3N2 Influenza Virus on Resistance to Oseltamivir

(2011) Mathilde Richard et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Replication inhibition activity of carbocycles related to oseltamivir on influenza A virus in vitro

(2011) Masahiro Niikura et al.   ANTIVIRAL RESEARCH

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

(2011) David B. Ascher et al.   BIOCHEMISTRY

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

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

(2011) Douglas EV Pires et al.   BMC GENOMICS

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Detection of E119V and E119I Mutations in Influenza A (H3N2) Viruses Isolated from an Immunocompromised Patient: Challenges in Diagnosis of Oseltamivir Resistance

(2010) M. Okomo-Adhiambo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors

(2010) Y. Koh et al.   JOURNAL OF VIROLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Emergence of a Multidrug-Resistant Pandemic Influenza A (H1N1) Virus

(2010) Erhard van der Vries et al.   NEW ENGLAND JOURNAL OF MEDICINE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Kinase mutations in human disease: interpreting genotype–phenotype relationships

(2009) Piya Lahiry et al.   NATURE REVIEWS GENETICS

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

(2008) Siew Chai et al.   BMC NEUROSCIENCE

Mechanisms of Acquired Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer

(2008) J. A. Engelman et al.   CLINICAL CANCER RESEARCH

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

(2008) Anthony L. Albiston et al.   FASEB JOURNAL

Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants

(2008) Patrick J. Collins et al.   NATURE

Activation of tyrosine kinases by mutation of the gatekeeper threonine

(2008) Mohammad Azam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA