Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

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

Understanding the structural and energetic basis of PD-1 and monoclonal antibodies bound to PD-L1: A molecular modeling perspective

(2018) Danfeng Shi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique

(2018) Cangzhi Jia et al.   BIOINFORMATICS

The molecular mechanism of two coreceptor binding site antibodies X5 and 17b neutralizing HIV-1: Insights from molecular dynamics simulation

(2018) Yan Zhang et al.   Chemical Biology & Drug Design

A Therapeutic Paradigm to Appraise the Competence of Chitosan Oligosaccharide Lactate Targeting Monoamine Oxidase-A and PGlycoprotein to Contest Depression by Channeling the Blood Brain Barrier

(2018) A. Anita Margret et al.   Current Bioinformatics

Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate

(2018) Chun Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Computational study of the binding mechanism between farnesoid X receptor α and antagonist N-benzyl-N-(3-(tertbutyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino) benzamide

(2018) Juan Du et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring the interactional details between aldose reductase (AKR1B1) and 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid through molecular dynamics simulations

(2018) Jiu-Yu Zhan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring the inhibition mechanism on HIF-2 by inhibitor PT2399 and 0X3 using molecular dynamics simulations

(2018) Dong-Ru Sun et al.   JOURNAL OF MOLECULAR RECOGNITION

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

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

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs` Species Origin, Druglikeness, Target and Pathway

(2018) Xiaofeng Li et al.   Anti-Cancer Agents in Medicinal Chemistry

Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters

(2018) Weiwei Xue et al.   CURRENT MEDICINAL CHEMISTRY

Computational study of the binding mechanism of medium chain acyl-CoA synthetase with substrate in Methanosarcina acetivorans

(2017) Juan Du et al.   JOURNAL OF BIOTECHNOLOGY

Uncoupling DAPK1 from NMDA receptor GluN2B subunit exerts rapid antidepressant-like effects

(2017) S-X Li et al.   MOLECULAR PSYCHIATRY

Identifying fast-onset antidepressants using rodent models

(2017) M J Ramaker et al.   MOLECULAR PSYCHIATRY

Comparison of computational model and X-ray crystal structure of human serotonin transporter: potential application for the pharmacology of human monoamine transporters

(2017) Fengyuan Yang et al.   MOLECULAR SIMULATION

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

Revealing vilazodone's binding mechanism underlying its partial agonism to the 5-HT1A receptor in the treatment of major depressive disorder

(2017) Guoxun Zheng et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites

(2016) Bertrand Simon et al.   STRUCTURE

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

(2016) Jingyu Xu et al.   Biomed Research International

Death Associated Protein Kinase 1 (DAPK1): A Regulator of Apoptosis and Autophagy

(2016) Pratibha Singh et al.   Frontiers in Molecular Neuroscience

The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective

(2016) Ying Hong Li et al.   PLoS One

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

(2016) Guoxun Zheng et al.   Scientific Reports

Identification of dual active agents targeting 5-HT1A and SERT by combinatorial virtual screening methods

(2015) Panpan Wang et al.   BIO-MEDICAL MATERIALS AND ENGINEERING

HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy

(2015) Quan Zou et al.   BIOINFORMATICS

Death Associated Protein Kinase (DAPK) -mediated neurodegenerative mechanisms in nematode excitotoxicity

(2015) John S Del Rosario et al.   BMC NEUROSCIENCE

Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

(2015) Theo Vos et al.   LANCET

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

Combination Therapy with Monoamine Oxidase Inhibitors and Other Antidepressants or Stimulants: Strategies for the Management of Treatment-Resistant Depression

(2015) Samantha J. Thomas et al.   PHARMACOTHERAPY

Novel insights into DAPK autophagic signalling using peptide aptamer combinatorial protein-interaction screens

(2014) Craig Stevens et al.   Autophagy

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Identification and Characterization of a Small-Molecule Inhibitor of Death-Associated Protein Kinase 1

(2014) Theis S. Wilbek et al.   CHEMBIOCHEM

Insight into Structural Organization and Protein-Protein Interaction of Non Structural 3 (NS3) Proteins from Dengue Serotypes

(2014) Pratap Parida et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

NMDA receptor structures reveal subunit arrangement and pore architecture

(2014) Chia-Hsueh Lee et al.   NATURE

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Structural and functional diversity in the activity and regulation of DAPK-related protein kinases

(2013) Koen Temmerman et al.   FEBS Journal

Death Associated Protein Kinases: Molecular Structure and Brain Injury

(2013) Syam Nair et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Melatonergic System in Mood and Anxiety Disorders and the Role of Agomelatine: Implications for Clinical Practice

(2013) Domenico De Berardis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Involvement of the GluN2A and GluN2B Subunits in Synaptic and Extrasynaptic N -methyl-d-aspartate Receptor Function and Neuronal Excitotoxicity

(2013) Xianju Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PaGeFinder: quantitative identification of spatiotemporal pattern genes

(2012) J.-B. Pan et al.   BIOINFORMATICS

Computational Prediction of Protein Hot Spot Residues

(2012) John Kenneth Morrow et al.   CURRENT PHARMACEUTICAL DESIGN

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces

(2012) Brandon S. Zerbe et al.   Journal of Chemical Information and Modeling

Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis

(2012) Weiwei Xue et al.   Molecular BioSystems

Drug Discovery Prospect from Untapped Species: Indications from Approved Natural Product Drugs

(2012) Feng Zhu et al.   PLoS One

Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors

(2011) Erkan Karakas et al.   NATURE

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

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

Stroke intervention pathways: NMDA receptors and beyond

(2011) Ted Weita Lai et al.   TRENDS IN MOLECULAR MEDICINE

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

(2010) Xiaofan Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Trends in the Exploration of Anticancer Targets and Strategies in Enhancing the Efficacy of Drug Targeting

(2010) F. Zhu et al.   Current Molecular Pharmacology

Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit

(2009) Erkan Karakas et al.   EMBO JOURNAL

What Are Next Generation Innovative Therapeutic Targets? Clues from Genetic, Structural, Physicochemical, and Systems Profiles of Successful Targets

(2009) F. Zhu et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

(2009) Huanxiang Liu et al.   MOLECULAR PHARMACEUTICS

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

Identification of hot-spot residues in protein-protein interactions by computational docking

(2008) Solène Grosdidier et al.   BMC BIOINFORMATICS

Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines

(2008) Y. Chen et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Comparison of computational approaches for predicting the effects of missense mutations on p53 function

(2008) Lillian T. Chong et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING