Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram

Understanding the Polypharmacological Profiles of Triple Reuptake Inhibitors by Molecular Simulation

(2021) Gao Tu et al.   ACS Chemical Neuroscience

Pharmacometabonomics: data processing and statistical analysis

(2021) Jianbo Fu et al.   BRIEFINGS IN BIOINFORMATICS

Cross-reactivity of two human IL-6 family cytokines OSM and LIF explored by protein-protein docking and molecular dynamics simulation

(2021) Qingqing Du et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter

(2021) Per Plenge et al.   Nature Communications

RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection

(2021) Song Zhang et al.   BRIEFINGS IN BIOINFORMATICS

SYNBIP: synthetic binding proteins for research, diagnosis and therapy

(2021) Xiaona Wang et al.   NUCLEIC ACIDS RESEARCH

VARIDT 2.0: structural variability of drug transporter

(2021) Tingting Fu et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

Allosteric Modulation of Neurotransmitter Transporters as a Therapeutic Strategy

(2020) Marco Niello et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The mechanism of a high-affinity allosteric inhibitor of the serotonin transporter

(2020) Per Plenge et al.   Nature Communications

MetaFS: Performance assessment of biomarker discovery in metaproteomics

(2020) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Artificial intelligence and machine learning‐aided drug discovery in central nervous system diseases: State‐of‐the‐arts and future directions

(2020) Sezen Vatansever et al.   MEDICINAL RESEARCH REVIEWS

MMEASE: Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis

(2020) Qingxia Yang et al.   Journal of Proteomics

Substrate and inhibitor binding to the serotonin transporter: Insights from computational, crystallographic, and functional studies

(2019) Talia Zeppelin et al.   NEUROPHARMACOLOGY

Predicting Drug-target Interactions via FM-DNN Learning

(2019) Jihong Wang et al.   Current Bioinformatics

Predicting drug side effects with compact integration of heterogeneous networks

(2019) Xian Zhao et al.   Current Bioinformatics

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

MoABank: An Integrated Database for Drug Mode of Action Knowledge

(2019) Yu Di Liao et al.   Current Bioinformatics

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

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Monoamine transporters: structure, intrinsic dynamics and allosteric regulation

(2019) Mary Hongying Cheng et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein Function Prediction: From Traditional Classifier to Deep Learning

(2019) Zhibin Lv et al.   PROTEOMICS

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

Identification Of Novel Key Targets And Candidate Drugs In Oral Squamous Cell Carcinoma

(2019) Juan Liu et al.   Current Bioinformatics

Relevance of Molecular Docking Studies in Drug Designing

(2019) Ritu Jakhar et al.   Current Bioinformatics

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

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

(2018) Tingting Fu et al.   ACS Chemical Neuroscience

Analysis of the Relative Movements Between EGFR and Drug Inhibitors Based on Molecular Dynamics Simulation

(2018) Lijiang Chen et al.   Current Bioinformatics

Steered Molecular Dynamics Simulation in Rational Drug Design

(2018) Phuc-Chau Do et al.   Journal of Chemical Information and Modeling

Structural basis for recognition of diverse antidepressants by the human serotonin transporter

(2018) Jonathan A. Coleman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

(2018) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

(2018) Feng Zhu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Structural basis for recognition of diverse antidepressants by the human serotonin transporter

(2018) Jonathan A. Coleman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

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

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

Proteome Mining For The Identification Of Putative Drug Targets For Human Pathogen Clostridium Tetani

(2018) Anum Munir et al.   Current Bioinformatics

In-silico identification of drug lead molecule against pesticide-exposed neurodevelopmental disorders through the network-based computational model approach

(2018) Neha Srivastava et al.   Current Bioinformatics

Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics

(2018) Ara M. Abramyan et al.   NEUROPHARMACOLOGY

Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study

(2017) Ismail Erol et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer

(2017) Suraj Adhikary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis and inhibitory evaluation of 3-linked imipramines for the exploration of the S2 site of the human serotonin transporter

(2016) Anne Brinkø et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Exploration of insights, opportunities and caveats provided by the X-ray structures of hSERT

(2016) Sid Topiol et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure-activity relationship studies of citalopram derivatives: examining substituents conferring selectivity for the allosteric site in the 5-HT transporter

(2016) M Andreas B Larsen et al.   BRITISH JOURNAL OF PHARMACOLOGY

X-ray structures and mechanism of the human serotonin transporter

(2016) Jonathan A. Coleman et al.   NATURE

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

(2016) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations

(2016) Yuzhen Niu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

(2016) Ying Hong Li et al.   PLoS One

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

(2016) Samuel Hertig et al.   PLoS Computational Biology

Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study

(2016) Guoxun Zheng et al.   Scientific Reports

Mechanism of Paroxetine (Paxil) Inhibition of the Serotonin Transporter

(2016) Bruce A. Davis et al.   Scientific Reports

Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites

(2015) Rong Zhu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Designing modulators of monoamine transporters using virtual screening techniques

(2015) Ole V. Mortensen et al.   Frontiers in Pharmacology

A comparative review of escitalopram, paroxetine, and sertraline

(2014) Connie Sanchez et al.   INTERNATIONAL CLINICAL PSYCHOPHARMACOLOGY

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

Future Directions for Serotonin and Antidepressants

(2013) Francesc Artigas   ACS Chemical Neuroscience

Unbinding Pathways from the Glucocorticoid Receptor Shed Light on the Reduced Sensitivity of Glucocorticoid Ligands to a Naturally Occurring, Clinically Relevant Mutant Receptor

(2013) Anna Maria Capelli et al.   JOURNAL OF MEDICINAL CHEMISTRY

SLC6 transporters: Structure, function, regulation, disease association and therapeutics

(2013) Akula Bala Pramod et al.   MOLECULAR ASPECTS OF MEDICINE

X-ray structure of dopamine transporter elucidates antidepressant mechanism

(2013) Aravind Penmatsa et al.   NATURE

Identification of an allosteric modulator of the serotonin transporter with novel mechanism of action

(2013) Sandhya Kortagere et al.   NEUROPHARMACOLOGY

Interaction of Antidepressants with the Serotonin and Norepinephrine Transporters

(2012) Lena Sørensen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Steric Hindrance Mutagenesis in the Conserved Extracellular Vestibule Impedes Allosteric Binding of Antidepressants to the Serotonin Transporter

(2012) Per Plenge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation

(2011) A. S. Kristensen et al.   PHARMACOLOGICAL REVIEWS

Molecular determinants for selective recognition of antidepressants in the human serotonin and norepinephrine transporters

(2011) J. Andersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting

(2011) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Escitalopram, an antidepressant with an allosteric effect at the serotonin transporter—a review of current understanding of its mechanism of action

(2011) Huailing Zhong et al.   PSYCHOPHARMACOLOGY

Binding and Orientation of Tricyclic Antidepressants within the Central Substrate Site of the Human Serotonin Transporter

(2009) Steffen Sinning et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Binding of Serotonin to the Human Serotonin Transporter. Molecular Modeling and Experimental Validation

(2008) Leyla Celik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Mechanism of a Neurotransmitter:Sodium Symporter—Inward Release of Na+ and Substrate Is Triggered by Substrate in a Second Binding Site

(2008) Lei Shi et al.   MOLECULAR CELL