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Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery

Current topics in medicinal chemistry, 2017-01, Vol.17 (23), p.2586

2017

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Journal of the American Chemical Society, 2015-02, Vol.137 (7), p.2695-2703

2015

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Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein–Protein Interaction Interfaces

Journal of chemical information and modeling, 2018-04, Vol.58 (4), p.784-793

2018

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Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

Proteins, structure, function, and bioinformatics, 2012-03, Vol.80 (3), p.871-883

2012

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What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?

Pharmacological reviews, 2015-01, Vol.67 (1), p.198-213

2015

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High‐energy water sites determine peptide binding affinity and specificity of PDZ domains

Protein science, 2009-08, Vol.18 (8), p.1609-1619

2009

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Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia

Nature communications, 2019-06, Vol.10 (1), p.2691-15, Article 2691

2019

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A Comprehensive Structure-Based Alignment of Prokaryotic and Eukaryotic Neurotransmitter/Na+ Symporters (NSS) Aids in the Use of the LeuT Structure to Probe NSS Structure and Function

Molecular pharmacology, 2006-11, Vol.70 (5), p.1630-1642

2006

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The binding sites for cocaine and dopamine in the dopamine transporter overlap

Nature neuroscience, 2008-07, Vol.11 (7), p.780-789

2008

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Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite

Methods in molecular biology (Clifton, N.J.), 2017, Vol.1561, p.235

2017

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Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

Nature communications, 2015-11, Vol.6 (1), p.8911, Article 8911

2015

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PDZBase: a protein–protein interaction database for PDZ-domains

Bioinformatics, 2005-03, Vol.21 (6), p.827-828

2005

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Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

ACS omega, 2016-08, Vol.1 (2), p.293-304

2016

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Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD

Proceedings of the National Academy of Sciences - PNAS, 2010-01, Vol.107 (1), p.413-418

2010

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Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

Journal of chemical information and modeling, 2012-12, Vol.52 (12), p.3263-3277

2012

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A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins

Bioinformatics, 2004-08, Vol.20 (12), p.1822-1835

2004

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State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum

The Journal of biological chemistry, 2006-09, Vol.281 (36), p.26444-26454

2006

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Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

Communications chemistry, 2020-06, Vol.3 (1), p.69-69, Article 69

2020

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Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein–coupled receptors

Proceedings of the National Academy of Sciences - PNAS, 2011-07, Vol.108 (30), p.E342-E342

2011

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Improved Docking of Polypeptides with Glide

Journal of chemical information and modeling, 2013-07, Vol.53 (7), p.1689-1699

2013

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Rigorous Free Energy Simulations in Virtual Screening

Journal of chemical information and modeling, 2020-09, Vol.60 (9), p.4153-4169

2020

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Editorial: Computer Aided Structure-based Lead Optimization

Current topics in medicinal chemistry, 2017-09, Vol.17 (23)

2017

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Molecular Determinants for the Complex Binding Specificity of the PDZ Domain in PICK1

The Journal of biological chemistry, 2005-05, Vol.280 (21), p.20539-20548

2005

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Ligand-Dependent Activation and Deactivation of the Human Adenosine A 2A Receptor

Journal of the American Chemical Society, 2013-06, Vol.135 (23), p.8749-8759

2013

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Relative Binding Free Energy Calculations Applied to Protein Homology Models

Journal of chemical information and modeling, 2016-12, Vol.56 (12), p.2388-2400

2016

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Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein–Protein Interaction Interfaces

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?

High‐energy water sites determine peptide binding affinity and specificity of PDZ domains

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia

A Comprehensive Structure-Based Alignment of Prokaryotic and Eukaryotic Neurotransmitter/Na+ Symporters (NSS) Aids in the Use of the LeuT Structure to Probe NSS Structure and Function

The binding sites for cocaine and dopamine in the dopamine transporter overlap

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

PDZBase: a protein–protein interaction database for PDZ-domains

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins

State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein–coupled receptors

Improved Docking of Polypeptides with Glide

Rigorous Free Energy Simulations in Virtual Screening

Editorial: Computer Aided Structure-based Lead Optimization

Molecular Determinants for the Complex Binding Specificity of the PDZ Domain in PICK1

Ligand-Dependent Activation and Deactivation of the Human Adenosine A 2A Receptor

Relative Binding Free Energy Calculations Applied to Protein Homology Models

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