Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies

Evaluating the stability of pharmacophore features using molecular dynamics simulations

(2016) Marcus Wieder et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Potent Human Telomerase Inhibitors: Molecular Dynamic Simulations, Multiple Pharmacophore-Based Virtual Screening, and Biochemical Assays

(2015) Faezeh Shirgahi Talari et al.   Journal of Chemical Information and Modeling

Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase

(2015) Chinmayee Choudhury et al.   Journal of Chemical Information and Modeling

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

(2015) Francesca Spyrakis et al.   Journal of Chemical Information and Modeling

Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes

(2015) Mauricio G. S. Costa et al.   Journal of Chemical Theory and Computation

Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why

(2015) Eggert Rühmann et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ligand-based modeling followed by in vitro bioassay yielded new potent glucokinase activators

(2015) Mutasem O. Taha et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors

(2014) Sivakumar Prasanth Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators

(2014) Mutasem O. Taha et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of novel urokinase plasminogen activator (uPA) inhibitors using ligand-based modeling and virtual screening followed by in vitro analysis

(2014) Mahmoud A. Al-Sha’er et al.   JOURNAL OF MOLECULAR MODELING

Elaborate ligand-based modeling reveals new human neutrophil elastase inhibitors

(2014) Maha Habash et al.   MEDICINAL CHEMISTRY RESEARCH

Molecular Dynamics Simulation Study of Conformational Changes of Transcription Factor TFIIS during RNA Polymerase II Transcriptional Arrest and Reactivation

(2014) Changsun Eun et al.   PLoS One

Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods

(2013) Balder Lai et al.   Journal of Chemical Information and Modeling

Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors

(2013) Sawsan Abuhamdah et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Pharmacophore modeling, homology modeling, and in silico screening reveal mammalian target of rapamycin inhibitory activities for sotalol, glyburide, metipranolol, sulfamethizole, glipizide, and pioglitazone

(2013) Mohammad A. Khanfar et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Elaborate ligand-based modeling reveal new migration inhibitory factor inhibitors

(2013) Mahmoud A. Al-Sha’er et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin

(2013) Ayse Ozlem Aykut et al.   PLoS Computational Biology

GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods

(2012) Simon Cross et al.   Journal of Chemical Information and Modeling

Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors

(2012) Mahmoud A. Al-Sha’er et al.   JOURNAL OF MOLECULAR MODELING

Elaborate ligand-based modeling and subsequent synthetic exploration unveil new nanomolar Ca2+/calmodulin-dependent protein kinase II inhibitory leads

(2011) Rand Shahin et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Discovery of New Antifungal Leads via Pharmacophore Modeling and QSAR Analysis of Fungal N-Myristoyl Transferase Inhibitors Followed by In Silico Screening

(2011) Mutasem O. Taha et al.   Chemical Biology & Drug Design

Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies

(2011) Mutasem O. Taha et al.   Journal of Chemical Information and Modeling

Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors

(2011) Rand Shahin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of new renin inhibitory leads via sequential pharmacophore modeling, QSAR analysis, in silico screening and in vitro evaluation

(2011) Afaf H. Al-Nadaf et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

(2011) Marijn P. A. Sanders et al.   MedChemComm

Tackling the challenges posed by target flexibility in drug design

(2010) Christian Beier et al.   Expert Opinion on Drug Discovery

Ligand-based and structure-based approaches in identifying ideal pharmacophore against c-Jun N-terminal kinase-3

(2010) B. V. S. Suneel Kumar et al.   JOURNAL OF MOLECULAR MODELING

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enhancing Drug Discovery Through In Silico Screening: Strategies to Increase True Positives Retrieval Rates

(2008) J. Kirchmair et al.   CURRENT MEDICINAL CHEMISTRY

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

(2008) Johannes Kirchmair et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN