In silico identification and design of potent peptide inhibitors against PDZ-3 domain of Postsynaptic Density Protein (PSD-95)

Combined pharmacophore, virtual screening and molecular dynamics studies to identify Bruton’s tyrosine kinase inhibitors

(2018) Seethalakshmi Sakthivel et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β

(2018) Akhil Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening, molecular docking and molecular dynamics

(2018) Rakesh Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

In search of AKT kinase inhibitors as anticancer agents: structure-based design, docking, and molecular dynamics studies of 2,4,6-trisubstituted pyridines

(2017) Pedro Josué Trejo-Soto et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Molecular dynamics simulation and molecular docking studies of 1,4-Dihydropyridines as P-glycoprotein’s allosteric inhibitors

(2017) Omolbanin Shahraki et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Atomic insight into designed carbamate-based derivatives as acetylcholine esterase (AChE) inhibitors: a computational study by multiple molecular docking and molecular dynamics simulation

(2017) Tecush Mohammadi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Dissociation of nNOS from PSD-95 promotes functional recovery after cerebral ischaemia in mice through reducing excessive tonic GABA release from reactive astrocytes

(2017) Yu-Hui Lin et al.   JOURNAL OF PATHOLOGY

Protection of neuronal cells from excitotoxicity by disrupting nNOS-PSD95 interaction with a small molecule SCR-4026

(2016) Shi-Fu Mo et al.   BRAIN RESEARCH

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanning

(2014) C. Paissoni et al.   COMPUTER PHYSICS COMMUNICATIONS

Structure-Based Multiscale Approach for Identification of Interaction Partners of PDZ Domains

(2014) Garima Tiwari et al.   Journal of Chemical Information and Modeling

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Supertertiary Structure of the MAGUK Core from PSD-95

(2013) Jun Zhang et al.   STRUCTURE

Design of Peptidomimetics for Inhibition of HER2 Receptor Dimerization by a Combination of Virtual Screening, MD Simulations, and QSARIn SilicoMethods

(2012) Mostafa Jamalan et al.   Chemical Biology & Drug Design

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains

(2012) Stefano Mostarda et al.   PLoS Computational Biology

Perturbing PSD-95 Interactions With NR2B-subtype Receptors Attenuates Spinal Nociceptive Plasticity and Neuropathic Pain

(2011) Richard D'Mello et al.   MOLECULAR THERAPY

Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease

(2010) Vladimir Frecer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95

(2010) Li Zhou et al.   NATURE MEDICINE

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coupling Molecular Dynamics Simulations with Experiments for the Rational Design of Indolicidin-Analogous Antimicrobial Peptides

(2009) Ching-Wei Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Hidden dynamic allostery in a PDZ domain

(2009) C. M. Petit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RhoA-associated protein Citron-N controls dendritic spine maintenance by interacting with spine-associated Golgi compartments

(2008) Paola Camera et al.   EMBO REPORTS

MAGUK proteins: New targets for pharmacological intervention in the glutamatergic synapse

(2008) Fabrizio Gardoni   EUROPEAN JOURNAL OF PHARMACOLOGY

Specific Targeting of Pro-Death NMDA Receptor Signals with Differing Reliance on the NR2B PDZ Ligand

(2008) F. X. Soriano et al.   JOURNAL OF NEUROSCIENCE

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cell-permeable Peptide Tat-PSD-95 PDZ2 Inhibits Chronic Inflammatory Pain Behaviors in Mice

(2008) Feng Tao et al.   MOLECULAR THERAPY

Reassessing a sparse energetic network within a single protein domain

(2008) C. N. Chi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA