VARIDT 2.0: structural variability of drug transporter

Upregulation of histone acetylation reverses organic anion transporter 2 repression and enhances 5-fluorouracil sensitivity in hepatocellular carcinoma

(2021) Yingying Wang et al.   BIOCHEMICAL PHARMACOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

(2020) Fengcheng Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Epigenetic Mechanisms Underlying Organic Solute Transporter β Repression in Colorectal Cancer

(2020) Ying Zhou et al.   MOLECULAR PHARMACOLOGY

Microbial Chassis Development for Natural Product Biosynthesis

(2020) Xianhao Xu et al.   TRENDS IN BIOTECHNOLOGY

Influences of ABC transporter and CYP3A4/5 genetic polymorphisms on the pharmacokinetics of lenvatinib in Chinese healthy subjects

(2020) Jiaming Li et al.   EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY

Drosophila SLC22 Orthologs Related to OATs, OCTs, and OCTNs Regulate Development and Responsiveness to Oxidative Stress

(2020) Darcy C. Engelhart et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

Targeting renal OATs to develop renal protective agent from traditional Chinese medicines: Protective effect of Apigenin against Imipenem‐induced nephrotoxicity

(2020) Xiaokui Huo et al.   PHYTOTHERAPY RESEARCH

ABCG2 transports anticancer drugs via a closed-to-open switch

(2020) Benjamin J. Orlando et al.   Nature Communications

Cooperative transport mechanism of human monocarboxylate transporter 2

(2020) Bo Zhang et al.   Nature Communications

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information

(2020) Fuyi Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Interactions between Oroxylin A with the solute carrier transporters and ATP-binding cassette transporters: Drug transporters profile for this flavonoid

(2020) Guanghui Ren et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Human organoids: model systems for human biology and medicine

(2020) Jihoon Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The involvement of human organic anion transporting polypeptides (OATPs) in drug-herb/food interactions

(2020) Youmna Ali et al.   Chinese Medicine

Chemical and structural investigation of the paroxetine-human serotonin transporter complex

(2020) Jonathan A Coleman et al.   eLife

A Method for Identifying Vesicle Transport Proteins Based on LibSVM and MRMD

(2020) Zhiyu Tao et al.   Computational and Mathematical Methods in Medicine

Impaired Transport Activity of Human Organic Anion Transporters (OATs) and Organic Anion Transporting Polypeptides (OATPs) by Wnt Inhibitors

(2020) Youmna Ali et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

ExoceRNA atlas: A database of cancer ceRNAs in human blood exosomes

(2020) Lei Xu et al.   LIFE SCIENCES

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges

(2020) Ai-Ming Yu et al.   PHARMACOLOGICAL REVIEWS

Cryo-EM structures reveal distinct mechanisms of inhibition of the human multidrug transporter ABCB1

(2020) Kamil Nosol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of human monocarboxylate transporter 1 inhibition by anti-cancer drug candidates

(2020) Nan Wang et al.   CELL

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Integrative modeling of membrane-associated protein assemblies

(2020) Jorge Roel-Touris et al.   Nature Communications

Structural insight into substrate and inhibitor discrimination by human P-glycoprotein

(2019) Amer Alam et al.   SCIENCE

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

(2019) Yang Zhang et al.   ACS Chemical Neuroscience

Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

(2019) Jing Tang et al.   MOLECULAR & CELLULAR PROTEOMICS

Functional characterization of 3D protein structures informed by human genetic diversity

(2019) Michael Hicks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the gene signature reflecting schizophrenia’s etiology by constructing artificial intelligence‐based method of enhanced reproducibility

(2019) Qing‐Xia Yang et al.   CNS Neuroscience & Therapeutics

ICD-11

(2019) The Lancet   LANCET

Inward-facing conformation of a multidrug resistance MATE family transporter

(2019) Sandra Zakrzewska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalpol Alleviates Adriamycin‐Induced Nephropathy by Activating the SIRT1 Signalling Pathway In Vivo and In Vitro

(2019) Jiangnan Zhang et al.   BRITISH JOURNAL OF PHARMACOLOGY

Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors

(2019) Suvamay Jana et al.   Journal of Chemical Information and Modeling

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies

(2019) Qingxia Yang et al.   BRIEFINGS IN BIOINFORMATICS

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

Structure and drug resistance of the Plasmodium falciparum transporter PfCRT

(2019) Jonathan Kim et al.   NATURE

10-Year Update on Study Results Submitted to ClinicalTrials.gov

(2019) Deborah A. Zarin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Bioengineered miR-328-3p modulates GLUT1-mediated glucose uptake and metabolism to exert synergistic antiproliferative effects with chemotherapeutics

(2019) Wanrong Yi et al.   Acta Pharmaceutica Sinica B

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

(2018) Jiangning Song et al.   BRIEFINGS IN BIOINFORMATICS

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation

(2018) Youngjin Kim et al.   SCIENCE

PharmGKB: A worldwide resource for pharmacogenomic information

(2018) Julia M. Barbarino et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Inward- and outward-facing homology modeling of human concentrative nucleoside transporter 3 (hCNT3) predicts an elevator-type transport mechanism

(2018) Sylvia Y. M. Yao et al.   Channels

Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis

(2018) Zhi-Jie Han et al.   CNS Neuroscience & Therapeutics

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

Influence of OCT1 Ontogeny and Genetic Variation on Morphine Disposition in Critically Ill Neonates: Lessons From PBPK Modeling and Clinical Study

(2018) David Hahn et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

OMIM.org: leveraging knowledge across phenotype–gene relationships

(2018) Joanna S Amberger et al.   NUCLEIC ACIDS RESEARCH

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

(2018) Thomas D Newport et al.   NUCLEIC ACIDS RESEARCH

EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins

(2018) Edoardo Sarti et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

(2018) Ying Hong Li et al.   BRIEFINGS IN BIOINFORMATICS

Computational design of ligand-binding membrane receptors with high selectivity

(2017) Xiang Feng et al.   Nature Chemical Biology

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

(2017) Hedvig Tordai et al.   Database-The Journal of Biological Databases and Curation

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

(2016) Yinglong Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic activation of the drug transporter OCT2 sensitizes renal cell carcinoma to oxaliplatin

(2016) Yanqing Liu et al.   Science Translational Medicine

ABCC1 confers tissue-specific sensitivity to cortisol versus corticosterone: A rationale for safer glucocorticoid replacement therapy

(2016) Mark Nixon et al.   Science Translational Medicine

Prediction of drug–ABC-transporter interaction — Recent advances and future challenges

(2015) Floriane Montanari et al.   ADVANCED DRUG DELIVERY REVIEWS

TheSCN1AMutation Database: Updating Information and Analysis of the Relationships among Genotype, Functional Alteration, and Phenotype

(2015) Heng Meng et al.   HUMAN MUTATION

Homology modeling of larger proteins guided by chemical shifts

(2015) Yang Shen et al.   NATURE METHODS

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling

(2015) Lora Mak et al.   Journal of Cheminformatics

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)

(2014) Gabriel Studer et al.   BIOINFORMATICS

The ABCs of membrane transporters in health and disease (SLC series): Introduction

(2013) Matthias A. Hediger et al.   MOLECULAR ASPECTS OF MEDICINE

The Transformer database: biotransformation of xenobiotics

(2013) Michael F. Hoffmann et al.   NUCLEIC ACIDS RESEARCH

HMPAS: Human Membrane Protein Analysis System

(2013) Min-Sung Kim et al.   Proteome Science

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

The UCSF-FDA TransPortal: A Public Drug Transporter Database

(2012) K M Morrissey et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters

(2012) Lars Geffers et al.   NUCLEIC ACIDS RESEARCH

Structure and permeation mechanism of a mammalian urea transporter

(2012) E. J. Levin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug Transporters in Drug Efficacy and Toxicity

(2011) M.K. DeGorter et al.   Annual Review of Pharmacology and Toxicology

Membrane transporters in drug development

(2010)   NATURE REVIEWS DRUG DISCOVERY

Overcoming the challenges of membrane protein crystallography

(2008) Elisabeth P Carpenter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY