T. Beuming

发表

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

Harel Weinstein, Thijs Beuming, Irina S Moreira, 2009, Proceedings of the National Academy of Sciences.

A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding

H. Weinstein, Lei Shi, J. Javitch, 2005, Neuropharmacology.

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.

Jennifer L. Knight, Markus K. Dahlgren, Edward D Harder, 2015, Journal of the American Chemical Society.

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

Sun Mi Park, Levi N. Naden, Steven K. Albanese, 2019, Nature Communications.

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

Sun Mi Park, Levi N. Naden, Steven K. Albanese, 2018, bioRxiv.

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

Amanda L. Jonsson, G. Voth, J. Shelley, 2013, Journal of the American Chemical Society.

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

H. Weinstein, Lei Shi, J. Javitch, 2008, Nature Neuroscience.

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor.

C. Higgs, W. Sherman, T. Beuming, 2010, ACS medicinal chemistry letters.

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

W. Sherman, V. Shanmugasundaram, Robert Abel, 2011, Proteins.

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

Woody Sherman, Thijs Beuming, Ramy Farid, 2009, Protein science : a publication of the Protein Society.

Databases and ontologies PDZBase : a protein – protein interaction database for PDZ-domains

H. Weinstein, M. Niv, P. Mukherjee, 2005 .

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

Harel Weinstein, Thijs Beuming, Jonathan A Javitch, 2006, Molecular Pharmacology.

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

Harel Weinstein, Lei Shi, Thijs Beuming, 2006, Journal of Biological Chemistry.

Discovery and Characterization of a G Protein – Biased Agonist That Inhibits b-Arrestin Recruitment to the D 2 Dopamine Receptor s

M. Ferrer, D. Sibley, Noel Southall, 2014 .

Discovery and Characterization of a G Protein–Biased Agonist That Inhibits β-Arrestin Recruitment to the D2 Dopamine Receptor

M. Ferrer, D. Sibley, Noel Southall, 2014, Molecular Pharmacology.

Are Deep Learning Structural Models Sufficiently Accurate for Free Energy Calculations? Application of FEP+ to AlphaFold2 Predicted Structures

V. Guallar, T. Beuming, Helena Martín, 2022, bioRxiv.

Design, Synthesis, and Optimization of Macrocyclic Peptides as Species-Selective Antimalaria Proteasome Inhibitors.

J. Vendôme, M. Michino, C. Nathan, 2022, Journal of medicinal chemistry.

What Can Crystal Structures of Aminergic Receptors Tell Us about Designing Subtype-Selective Ligands?

Lei Shi, Thijs Beuming, Mayako Michino, 2015, Pharmacological Reviews.

Improved Docking of Polypeptides with Glide

Woody Sherman, Ivan Tubert-Brohman, Matthew P. Repasky, 2013, J. Chem. Inf. Model..

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite.

Thijs Beuming, Jas Bhachoo, T. Beuming, 2017, Methods in molecular biology.

Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement

Woody Sherman, Daniele Pala, Thijs Beuming, 2013, J. Chem. Inf. Model..

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

Levi N. Naden, Steven K. Albanese, Derek S. Tan, 2018, bioRxiv.

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

Woody Sherman, Adriaan P. IJzerman, Robert Abel, 2016, ACS omega.

Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor

Woody Sherman, Adriaan P. IJzerman, Herman van Vlijmen, 2014, J. Chem. Inf. Model..

PDZBase: a protein?Cprotein interaction database for PDZ-domains

Lucy Skrabanek, Thijs Beuming, Masha Y. Niv, 2005, Bioinform..

Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma

Susan S. Taylor, S. Simon, Jiali Gao, 2018, Scientific Reports.

Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis

J. Sacchettini, T. Ioerger, J. Vendôme, 2018, ACS infectious diseases.

Loop prediction for a GPCR homology model: Algorithms and results

Richard A Friesner, Thijs Beuming, Dahlia A Goldfeld, 2013, Proteins.

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

G. Pruijn, W. Sherman, T. Beuming, 2020, Communications Chemistry.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

Chao Xu, J. Min, W. Sherman, 2015, Nature Communications.

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

H. Weinstein, M. Niv, Chiung-wen Chang, 2005, Journal of Biological Chemistry.

Predicting GPCR Promiscuity Using Binding Site Features

Woody Sherman, Anat Levit, Goran Krilov, 2014, J. Chem. Inf. Model..

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

Thijs Beuming, Harel Weinstein, H. Weinstein, 2004, Bioinform..

Relative Binding Free Energy Calculations Applied to Protein Homology Models

Daniel Cappel, Woody Sherman, Jun Qi, 2016, J. Chem. Inf. Model..

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor

Woody Sherman, Adriaan P. IJzerman, Herman van Vlijmen, 2016, Journal of Computer-Aided Molecular Design.

Rigorous Free Energy Simulations in Virtual Screening

Woody Sherman, Zoe Cournia, Thijs Beuming, 2020, J. Chem. Inf. Model..

Structure-Activity Relationship Studies of Antimalarial Plasmodium Proteasome Inhibitors─Part II.

M. Foley, J. Vendôme, N. Liverton, 2023, Journal of medicinal chemistry.

8R-lisuride is a potent stereospecific histamine H1-receptor partial agonist.

O. Zuiderveld, R. Leurs, U. Hacksell, 2004, Molecular pharmacology.

Molecular dynamics techniques for modeling G protein-coupled receptors.

Woody Sherman, Thijs Beuming, W. Sherman, 2016, Current opinion in pharmacology.

A Single Glycine in Extracellular Loop 1 Is the Critical Determinant for Pharmacological Specificity of Dopamine D2 and D3 Receptors

Lei Shi, J. Javitch, M. Michino, 2013, Molecular Pharmacology.

Molecular determinants of selectivity and efficacy at the dopamine D3 receptor.

Lei Shi, J. Javitch, M. Michino, 2012, Journal of medicinal chemistry.

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

H. Weinstein, Lei Shi, A. Newman, 2011, Neuropharmacology.

Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor.

Robert Abel, Lingle Wang, Richard A Friesner, 2015, The journal of physical chemistry. B.

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

Woody Sherman, Thijs Beuming, W. Sherman, 2012, J. Chem. Inf. Model..

Steric Hindrance Mutagenesis in the Conserved Extracellular Vestibule Impedes Allosteric Binding of Antidepressants to the Serotonin Transporter*

H. Weinstein, Lei Shi, A. Newman, 2012, The Journal of Biological Chemistry.

Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors

Richard A Friesner, Thijs Beuming, Dahlia A Goldfeld, 2011, Proceedings of the National Academy of Sciences.

A Structural Context for Studying Neurotransmitter Transporter Function

H. Weinstein, J. Javitch, T. Beuming, 2004 .

Development of a highly selective Plasmodium falciparum proteasome inhibitor with anti-malaria activity in humanized mice.

P. Rosenthal, J. Vendôme, M. Michino, 2021, Angewandte Chemie.

Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma

Susan S. Taylor, S. Simon, Jiali Gao, 2018, Scientific Reports.

Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures

V. Guallar, T. Beuming, Helena Martín, 2022, bioRxiv.

Probing conformational changes in neurotransmitter transporters: a structural context.

Orkun S. Soyer, Harel Weinstein, Thijs Beuming, 2003, European journal of pharmacology.

TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical Literature

Jonathan A. Javitch, Marko Srdanovic, Lucy Skrabanek, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement

W. Sherman, M. Mor, T. Beuming, 2013, J. Chem. Inf. Model..

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

Amanda L. Jonsson, G. Voth, J. Shelley, 2013, Journal of the American Chemical Society.

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

W. Sherman, T. Beuming, D. Cappel, 2017, Current topics in medicinal chemistry.

Conformational changes in dopamine transporter intracellular regions upon cocaine binding and dopamine translocation

H. Weinstein, Lei Shi, J. Javitch, 2014, Neurochemistry International.