M. Bodkin

发表

Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts

A. Bender, S. Liggi, Georgios Drakakis, 2013, Molecular informatics.

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

R. Glen, A. Bender, S. Liggi, 2014, Future medicinal chemistry.

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis.

Aakash Chavan Ravindranath, A. Bender, S. Liggi, 2015, Molecular bioSystems.

Modeling of ribonucleic acid–ligand interactions

Ewa I. Chudyk, M. Bodkin, J. Bujnicki, 2015 .

Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis

A. Bender, Georgios Drakakis, Adam E. Hendry, 2014 .

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders.

Peter V Coveney, Fouad S. Husseini, Alexander Heifetz, 2019, Journal of chemical theory and computation.

Accurate calculation of the absolute free energy of binding for drug molecules

Michael J. Bodkin, Philip C. Biggin, Matteo Aldeghi, 2015, Chemical science.

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

Philip C Biggin, Matteo Aldeghi, Stefan Knapp, 2016, Journal of the American Chemical Society.

Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties.

P. Biggin, M. Bodkin, A. Heifetz, 2016, Advances in experimental medicine and biology.

Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory.

Richard H. Henchman, Michael P. Mazanetz, M. Bodkin, 2016, The journal of physical chemistry. B.

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

M. Bodkin, J. Michel, A. Heifetz, 2015, Physical chemistry chemical physics : PCCP.

Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

M. Babu, M. Bodkin, Iñaki Morao, 2020, Journal of chemical theory and computation.

3D QSAR Methods: Phase and Catalyst Compared

David A. Evans, Thompson N. Doman, David A. Thorner, 2007, J. Chem. Inf. Model..

Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

Ewa I. Chudyk, M. Bodkin, Iñaki Morao, 2018, Methods in molecular biology.

Pharmaceutical Industry—Academia Cooperation

P. Coveney, M. Bodkin, Iñaki Morao, 2021, Recent Advances of the Fragment Molecular Orbital Method.

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

M. Bodkin, Iñaki Morao, A. Heifetz, 2020, Methods in molecular biology.

Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach.

M. Bodkin, Iñaki Morao, A. Heifetz, 2019, Current opinion in structural biology.

Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors.

Ewa I. Chudyk, P. McEwan, M. Bodkin, 2016, Journal of medicinal chemistry.

SuCOS is Better than RMSD for Evaluating Fragment Elaboration and Docking Poses

G. Morris, M. Bodkin, F. von Delft, 2019 .

Small-molecule modulators of serine protease inhibitor proteins (serpins).

M. Bodkin, T. Kellici, E. S. Pilka, 2020, Drug discovery today.

2-NAP: a selective, hydrophilic, non-peptide CCKA - receptor antagonist derived from the cholecystokinin C-terminal dipeptide.

M. Bodkin, C. Low, H. Broughton, 1993 .

The intactness and orientation of acetylcholine receptor-rich membrane from Torpedo californica electric tissue.

M. Bodkin, E. Holtzman, A. Karlin, 1989, Archives of biochemistry and biophysics.

Application of an Integrated GPCR SAR-Modeling Platform To Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B.

P. Biggin, M. Bodkin, Iñaki Morao, 2016, ACS chemical biology.

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Gregory A Ross, Gregory A. Ross, S. Knapp, 2018, Communications Chemistry.

Therapeutic Potential of Targeting Plasminogen Activator Inhibitor-1 in COVID-19

M. Bodkin, T. Kellici, E. S. Pilka, 2021, Trends in Pharmacological Sciences.

Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method

M. Bodkin, A. Heifetz, D. Fedorov, 2022, J. Chem. Inf. Model..

Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat.

Andreas Bender, Georgios Drakakis, Suzanne C Brewerton, 2017, ACS chemical biology.

Competing interactions contributing to alpha-helical stability in aqueous solution.

M. Bodkin, J. Goodfellow, 1995, Protein science : a publication of the Protein Society.

A new class of non-peptidic cholecystokinin-B/gastrin receptor antagonists based on dibenzobicyclo[2.2.2]octane.

M. Bodkin, C. Low, I. Buck, 1994, Journal of medicinal chemistry.

Janocchio—a Java applet for viewing 3D structures and calculating NMR couplings and NOEs

M. Bodkin, David A. Evans, G. Sharman, 2007, Magnetic resonance in chemistry : MRC.

Development and Application of a Data-Driven Reaction Classification Model: Comparison of an Electronic Lab Notebook and Medicinal Chemistry Literature

Dimitar Hristozov, James Webster, Michael J Bodkin, 2019, J. Chem. Inf. Model..

Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method.

M. Bodkin, S. Bromidge, A. Heifetz, 2020, Methods in molecular biology.

Competing interactions contributing to α‐helical stability in aqueous solution

M. Bodkin, J. Goodfellow, 1995 .

Hydrophobic solvation in aqueous trifluoroethanol solution.

M. Bodkin, J. Goodfellow, 1998, Biopolymers.

Learning protein-ligand binding affinity with atomic environment vectors

G. Morris, P. Biggin, M. Bodkin, 2020, Journal of Cheminformatics.

RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design

Gian Marco Ghiandoni, Dimitar Hristozov, M. Bodkin, 2021, Molecular informatics.

Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

Philip C Biggin, Matteo Aldeghi, Stefan Knapp, 2017, J. Chem. Inf. Model..

Fighting COVID-19 with Artificial Intelligence.

Tahsin F. Kellici, M. Bodkin, A. Heifetz, 2021, Methods in molecular biology.

Enhancing reaction-based de novo design using a multi-label reaction class recommender

Dimitar Hristozov, Valerie J. Gillet, Michael J. Bodkin, 2020, Journal of Computer-Aided Molecular Design.

3D QSAR Methods: Phase and Catalyst Compared.

Thompson N. Doman, David A. Thorner, Michael J. Bodkin, 2007 .

The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions

Michael J. Bodkin, Philip C. Biggin, Alexander Heifetz, 2016, J. Chem. Inf. Model..

Species Selectivity of a Nicotinic Acetylcholine Receptor Agonist Is Conferred by Two Adjacent Extracellular β4 Amino Acids that Are Implicated in the Coupling of Binding to Channel Gating

M. Bodkin, G. Young, E. Sher, 2007, Molecular Pharmacology.

Mining for Context‐Sensitive Bioisosteric Replacements in Large Chemical Databases

Peter Willett, Valerie J. Gillet, Michael J. Bodkin, 2012 .

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1–2 September 2014

Gebhard F. X. Schertler, Christofer S. Tautermann, Philip C. Biggin, 2015, Naunyn-Schmiedeberg's Archives of Pharmacology.

Guiding lead optimization with GPCR structure modeling and molecular dynamics.

Philip C Biggin, Tim James, Michael J Bodkin, 2016, Current opinion in pharmacology.

Using the fragment molecular orbital method to investigate agonist–orexin-2 receptor interactions

Philip C. Biggin, Matteo Aldeghi, Dmitri G. Fedorov, 2016, Biochemical Society transactions.

Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery.

Alexander Heifetz, Michelle Southey, Inaki Morao, 2018, Methods in molecular biology.

ChEMBLSpace - a graphical explorer of the chemogenomic space covered by the ChEMBL database

George Papadatos, David A. Evans, David A. Thorner, 2013, Bioinform..

Knowledge-Based Approach to de Novo Design Using Reaction Vectors

Valerie J. Gillet, Michael J. Bodkin, Hina Patel, 2009, J. Chem. Inf. Model..

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

R. Glen, A. Bender, Alexios Koutsoukas, 2014, Future medicinal chemistry.

Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts

A. Bender, Georgios Drakakis, Adam E. Hendry, 2013, Molecular informatics.

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis.

Hinrich W. H. Göhlmann, Aakash Chavan Ravindranath, A. Bender, 2015, Molecular bioSystems.

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1–2 September 2014

T. Ceska, P. Biggin, M. Bodkin, 2015, Naunyn-Schmiedeberg's Archives of Pharmacology.

Discovery of the First Selective, Nonpeptidic Orexin 2 Receptor Agonists.

P. Biggin, M. Bodkin, Alexander Heifetz, 2015, Journal of medicinal chemistry.

Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital‐based density‐functional tight‐binding method

Alexander Heifetz, Dmitri G. Fedorov, Roger Robinson, 2017, J. Comput. Chem..

Multiobjective De Novo Design of Synthetically Accessible Compounds

Dimitar Hristozov, Valerie J. Gillet, Michael J. Bodkin, 2013 .

Validation of Reaction Vectors for de novo Design

Dimitar Hristozov, Valerie J. Gillet, Michael J. Bodkin, 2012 .

Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors.

Ewa I. Chudyk, P. McEwan, M. Bodkin, 2016, Journal of medicinal chemistry.