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An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

Scientific reports, 2019-11, Vol.9 (1), p.16829-13, Article 16829

2019

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N501Y and K417N Mutations in the Spike Protein of SARS-CoV‑2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study

Journal of chemical information and modeling, 2021-12, Vol.61 (12), p.6079-6084

Fratev, Filip

2021

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R346K Mutation in the Mu Variant of SARS-CoV‑2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study

Journal of chemical information and modeling, 2022-02, Vol.62 (3), p.627-631

Fratev, Filip

2022

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Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations

Physical chemistry chemical physics : PCCP, 2015-05, Vol.17 (20), p.13403-13420

Fratev, Filip

2015

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Benzimidazoles Containing Piperazine Skeleton at C-2 Position as Promising Tubulin Modulators with Anthelmintic and Antineoplastic Activity

Pharmaceuticals (Basel, Switzerland), 2023-10, Vol.16 (11), p.1518

2023

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PPARγ helix 12 exhibits an antagonist conformation

Physical chemistry chemical physics : PCCP, 2016-04, Vol.18 (13), p.9272-9280

Fratev, Filip

2016

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Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies

ACS omega, 2018-04, Vol.3 (4), p.4357-4371

2018

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Structural and Dynamical Insight into PPARγ Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists

International journal of molecular sciences, 2015-07, Vol.16 (7), p.15405-15424

2015

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PPARγ helix 12 exhibits an antagonist conformationElectronic supplementary information (ESI) available. See DOI: 10.1039/c5cp06729d

Fratev, Filip

2016-03

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PPARγ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study

Journal of biomolecular structure & dynamics, 2017-02, Vol.35 (3), p.476-485

Fratev, Filip

2017

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Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulationsElectronic supplementary information (ESI) available: Movie 1: H12 conformational sampling in an ERα monomer based on simulation aMDm2, which describes the observed and activation helix populations under and above H11 presented in Fig. 1, respectively. Movie 2: transition of H12 from an unfolded form to an antagonist and then an antagonist conformation via Path

Fratev, Filip

2015-05

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An in silico study of the molecular basis of B-RAF activation and conformational stability

BMC structural biology, 2009-07, Vol.9 (1), p.47-47

2009

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Abstract 586: Development of a novel pan-chemokine receptor inhibitor as therapeutic for breast cancer

Cancer research (Chicago, Ill.), 2023-04, Vol.83 (7_Supplement), p.586-586

2023

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1H-benzimidazole-2-yl hydrazones as tubulin-targeting agents: Synthesis, structural characterization, anthelmintic activity and antiproliferative activity against MCF-7 breast carcinoma cells and molecular docking studies

Chemico-biological interactions, 2021-08, Vol.345, p.109540-109540, Article 109540

2021

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Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case

Journal of chemical information and modeling, 2014-05, Vol.54 (5), p.1524-1536

2014

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Elucidation of the orientation of selected drugs with 2-hydroxylpropyl-β-cyclodextrin using 2D-NMR spectroscopy and molecular modeling

International journal of pharmaceutics, 2018-07, Vol.545 (1-2), p.357-365

2018

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Discovery of new AKT1 inhibitors by combination of in silico structure based virtual screening approaches and biological evaluations

Journal of biomolecular structure & dynamics, 2021-01, Vol.39 (1), p.368-377

2021

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Discovery of GlyT2 Inhibitors Using Structure-Based Pharmacophore Screening and Selectivity Studies by FEP+ Calculations

ACS medicinal chemistry letters, 2019-06, Vol.10 (6), p.904-910

2019

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Molecular dynamics simulation of the human estrogen receptor alpha: contribution to the pharmacophore of the agonists

Mathematics and computers in simulation, 2017-03, Vol.133, p.124-134

2017

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Structural insight into the UNC-45-myosin complex

Proteins, structure, function, and bioinformatics, 2013-07, Vol.81 (7), p.1212-1221

2013

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Structural and Dynamical Insight into PPAR[gamma] Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists

International journal of molecular sciences, 2015-07, Vol.16 (7), p.15405

2015

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Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

Journal of chemical information and modeling, 2013-04, Vol.53 (4), p.923-937

2013

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A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals

Journal of molecular graphics & modelling, 2008-09, Vol.27 (2), p.147-160

2008

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Discovery of a Novel Selective PPAR? Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

Journal of chemical information and modeling, 2013-04, Vol.53 (4), p.923

2013

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3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones

Journal of chemical information and modeling, 2005-05, Vol.45 (3), p.634-644

2005

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An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

N501Y and K417N Mutations in the Spike Protein of SARS-CoV‑2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study

R346K Mutation in the Mu Variant of SARS-CoV‑2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study

Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations

Benzimidazoles Containing Piperazine Skeleton at C-2 Position as Promising Tubulin Modulators with Anthelmintic and Antineoplastic Activity

PPARγ helix 12 exhibits an antagonist conformation

Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies

Structural and Dynamical Insight into PPARγ Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists

PPARγ helix 12 exhibits an antagonist conformationElectronic supplementary information (ESI) available. See DOI: 10.1039/c5cp06729d

PPARγ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study

An in silico study of the molecular basis of B-RAF activation and conformational stability

Abstract 586: Development of a novel pan-chemokine receptor inhibitor as therapeutic for breast cancer

1H-benzimidazole-2-yl hydrazones as tubulin-targeting agents: Synthesis, structural characterization, anthelmintic activity and antiproliferative activity against MCF-7 breast carcinoma cells and molecular docking studies

Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case

Elucidation of the orientation of selected drugs with 2-hydroxylpropyl-β-cyclodextrin using 2D-NMR spectroscopy and molecular modeling

Discovery of new AKT1 inhibitors by combination of in silico structure based virtual screening approaches and biological evaluations

Discovery of GlyT2 Inhibitors Using Structure-Based Pharmacophore Screening and Selectivity Studies by FEP+ Calculations

Molecular dynamics simulation of the human estrogen receptor alpha: contribution to the pharmacophore of the agonists

Structural insight into the UNC-45-myosin complex

Structural and Dynamical Insight into PPAR[gamma] Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists

Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals

Discovery of a Novel Selective PPAR? Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones

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