Robert Abel

发表

Comparison of multiple Amber force fields and development of improved protein backbone parameters

V. Hornak, A. Roitberg, Asim Okur, 2006, Proteins.

Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions.

Edward D Harder, James M. Stevenson, Robert Abel, 2021, Journal of chemical theory and computation.

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

B. Berne, R. Friesner, R. Farid, 2008, Journal of the American Chemical Society.

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.

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Jennifer L. Knight, Markus K. Dahlgren, Edward D Harder, 2016, Journal of chemical theory and computation.

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

Edward D Harder, J. Mccammon, Robert Abel, 2015, Journal of chemical theory and computation.

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

R. Friesner, Kai Zhu, Suwen Zhao, 2011, Proteins.

Protein-Ligand Binding Free Energy Calculations with FEP.

Robert Abel, Lingle Wang, J. Chambers, 2019, Methods in molecular biology.

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.

Jennifer L. Knight, W. Sherman, Robert Abel, 2013, Journal of chemical theory and computation.

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.

Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability-Large-Scale Validation of MD-Based Relative Free Energy Calculations.

Woody Sherman, Robert Abel, Lingle Wang, 2017, Journal of molecular biology.

Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding

Robert Abel, Richard A Friesner, Byungchan Kim, 2007, Proceedings of the National Academy of Sciences.

Accelerating drug discovery through tight integration of expert molecular design and predictive scoring.

Robert Abel, Richard A Friesner, Sathesh Bhat, 2017, Current opinion in structural biology.

WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking.

Matthew P. Repasky, R. Friesner, R. Murphy, 2016, Journal of medicinal chemistry.

Sensitivity in binding free energies due to protein reorganization

Robert Abel, Lingle Wang, David L Mobley, 2016, bioRxiv.

Sensitivity in binding free energies due to protein reorganization

David L. Mobley, Robert Abel, Lingle Wang, 2016 .

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors.

Jérôme Hert, Robert Abel, Lingle Wang, 2017, Journal of medicinal chemistry.

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

Steven K. Albanese, J. Chodera, Robert Abel, 2017, bioRxiv.

Baseline Analysis of a Young &agr;-1-Antitrypsin Deficiency Liver Disease Cohort Reveals Frequent Portal Hypertension

P. Rosenthal, R. Arnon, C. Spino, 2015, Journal of pediatric gastroenterology and nutrition.

A pre-injector upgrade for ISIS, including a medium energy beam transport line and an RF-driven H− ion source

Robert Abel, O. Tarvainen, T. Sarmento, 2019, Review of Scientific Instruments.

The RF H− ion source project at RAL

Robert Abel, D. Noll, O. Tarvainen, 2018 .

Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein–Protein Interfaces

R. Friesner, Robert Abel, Lingle Wang, 2019, Journal of molecular biology.

Exploring the Activity Profile of TbrPDEB1 and hPDE4 Inhibitors Using Free Energy Perturbation

I. D. de Esch, Robert Abel, L. Zara, 2022, ACS medicinal chemistry letters.

AutoDesigner, a De Novo Design Algorithm for Rapidly Exploring Large Chemical Space for Lead Optimization: Application to the Design and Synthesis of d-Amino Acid Oxidase Inhibitors

Volker A. Eyrich, Robert Abel, Sathesh Bhat, 2022, J. Chem. Inf. Model..

Enhancing water sampling in free energy calculations with grand canonical Monte Carlo.

Gregory A Ross, Gregory A. Ross, Edward D Harder, 2020, Journal of chemical theory and computation.

Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization

Phani Ghanakota, Robert Abel, K. Leswing, 2020, J. Chem. Inf. Model..

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding.

Daniel J. Sindhikara, Matthew J. Grisewood, Steven V. Jerome, 2020, Journal of chemical theory and computation.

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models.

R. Friesner, K. Borrelli, Kai Zhu, 2022, Journal of chemical theory and computation.

High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations.

R. Friesner, M. Halls, James M. Stevenson, 2022, The journal of physical chemistry. B.

A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules

G. Tresadern, R. Farid, J. Greenwood, 2019 .

Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors

Markus K. Dahlgren, Ivan Tubert Brohman, A. Bortolato, 2019, J. Chem. Inf. Model..

Contribution of Explicit Solvent Effects to the Binding Affinity of Small‐Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

Woody Sherman, Robert Abel, Richard A Friesner, 2011, ChemMedChem.

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.

Robert Abel, Lingle Wang, Richard A. Friesner, 2019, Journal of chemical theory and computation.

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space.

Gregory A Ross, Markus K. Dahlgren, Gregory A. Ross, 2021, Journal of chemical theory and computation.

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1

Tongqing Zhou, Baoshan Zhang, Robert Abel, 2017, Journal of molecular biology.

Intraocular Penetration of Amoxicillin

Robert Abel, I. Leopold, G. L. Boyle, 1976 .

Development of an Artificial Cornea

Robert Abel, 1987 .

Protein side-chain dynamics and residual conformational entropy.

Robert Abel, Richard A Friesner, Mark Rance, 2009, Journal of the American Chemical Society.

Reticulocyte Response in Sickle Cell Anemia Treated With Recombinant Human Erythropoietin : A Double-Blind Study

G. Stamatoyannopoulos, R. Nagel, Robert Abel, 2003 .

F reticulocyte response in sickle cell anemia treated with recombinant human erythropoietin: a double-blind study

G. Stamatoyannopoulos, R. Nagel, Robert Abel, 1993 .

INTRAVENOU S ADENIN E ARABINOSIDE AGAINST HERPE S SIMPLEX KERATOUVEITIS IN HUMAN S

J. Sugar, Robert Abel, H. Kaufman, 1974 .

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

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

Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

Robert Abel, Richard Friesner, Thomas Steinbrecher, 2017, Journal of molecular biology.

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

Steven K. Albanese, J. Chodera, Robert Abel, 2017, bioRxiv.

Is structure based drug design ready for selectivity optimization?

Robert Abel, Lingle Wang, John D. Chodera, 2020, bioRxiv.

Free Energy Calculation Guided Virtual Screening of Synthetically Feasible Ligand R-Group and Scaffold Modifications: An Emerging Paradigm for Lead Optimization

Robert Abel, Sathesh Bhat, Robert Abel, 2017 .

Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity.

Michael R. Green, V. Seshan, Phani Ghanakota, 2019, JCI insight.

Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring

Kai Zhu, Robert Abel, Ramy Farid, 2014, J. Chem. Inf. Model..

Chapter 84 – Cataracts

Robert Abel, 2018 .

Capítulo 83 – Cataratas

Robert Abel, 2009 .

Four paths to computer animation: entertainment, broadcast, education and science - will their future converge? (panel session)

James F. Blinn, Robert Abel, Carl Rosendahl, 1988, SIGGRAPH.

Accurate Binding Free Energy Predictions in Fragment Optimization

Daniel Cappel, Woody Sherman, Robert Abel, 2015, J. Chem. Inf. Model..

Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods.

Robert Abel, Richard A. Friesner, Jennifer L. Knight, 2014, Journal of chemical theory and computation.

Computational methods for high resolution prediction and refinement of protein structures.

Robert Abel, Richard A Friesner, Edward B Miller, 2013, Current opinion in structural biology.

Conformational preferences underlying reduced activity of a thermophilic ribonuclease H.

Kate A. Stafford, R. Friesner, A. Palmer, 2015, Journal of molecular biology.

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges.

Robert Abel, Lingle Wang, Wei Chen, 2018, Journal of chemical theory and computation.

New hypotheses about the structure–function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor‐like repeat A docking site using WaterMap

Woody Sherman, Robert A Pearlstein, Robert Abel, 2010, Proteins.

Advancing Drug Discovery through Enhanced Free Energy Calculations.

Robert Abel, Lingle Wang, Richard A. Friesner, 2017, Accounts of chemical research.

Efficient Exploration of Chemical Space with Docking and Deep Learning.

Robert Abel, Matthew P. Repasky, Y Yang, 2021, Journal of chemical theory and computation.

Chapter 85 – Age-Related Macular Degeneration

Robert Abel, 2018 .

Capítulo 84 – Degeneración macular asociada a la edad

Robert Abel, 2009 .

Contributions of water transfer energy to protein‐ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

Woody Sherman, Robert A Pearlstein, Robert Abel, 2013, Proteins.

A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

Robert Abel, Lingle Wang, David L Mobley, 2017, Current topics in medicinal chemistry.

Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations.

Pratyush Tiwary, Shulu Feng, Robert Abel, 2016, Journal of chemical theory and computation.

Caesium capture by POCO CZR-2 graphite and characterisation experiments on VESPA

Robert Abel, O. Tarvainen, S. Lawrie, 2018 .

High current results from the 2X scaled Penning source

Robert Abel, O. Tarvainen, T. Sarmento, 2018 .

General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes.

Robert Abel, Lingle Wang, O. Ichihara, 2020, Journal of chemical theory and computation.

Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations.

R. Friesner, J. Vendôme, Robert Abel, 2023, Journal of chemical information and modeling.

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics

Robert Abel, Lingle Wang, Takayuki Kimura, 2019, J. Chem. Inf. Model..

Quantitatively Accounting for Protein Reorganization in Computer-Aided Drug Design.

K. Borrelli, Robert Abel, Lingle Wang, 2023, Journal of chemical theory and computation.

Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

Robert Abel, Lingle Wang, Daniel J. Sindhikara, 2017, Journal of chemical theory and computation.

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.

Robert Abel, Lingle Wang, Richard A Friesner, 2017, Journal of chemical theory and computation.

Lead optimization mapper: automating free energy calculations for lead optimization

Shuai Liu, David L. Mobley, Robert Abel, 2013, Journal of Computer-Aided Molecular Design.

Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

Bin W. Zhang, R. Levy, Robert Abel, 2018, The journal of physical chemistry letters.

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.

The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions

H. V. van Vlijmen, G. Tresadern, H. Geys, 2022, J. Chem. Inf. Model..

Application of Free Energy Perturbation (FEP+) to Understanding Ligand Selectivity: A Case Study to Assess Selectivity Between Pairs of Phosphodiesterases (PDE's)

Robert Abel, Francesca Moraca, Ana Negri, 2019, J. Chem. Inf. Model..

Simulating the LSST system

Victor L. Krabbendam, Steven M. Kahn, Robert Abel, 2010, Astronomical Telescopes + Instrumentation.

Modeling the value of predictive affinity scoring in preclinical drug discovery.

Robert Abel, Lingle Wang, Richard A Friesner, 2018, Current opinion in structural biology.

Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States.

Haoyu S. Yu, Robert Abel, Lingle Wang, 2018, Journal of chemical theory and computation.

11th German Conference on Chemoinformatics (GCC 2015)

Timothy Clark, Jonathan W. Essex, Peter Kolb, 2016, J. Cheminformatics.

Advancing Free Energy Calculations of Metalloenzyme in Drug Discovery via Implementation of LFMM Potentials.

Edward D Harder, Haoyu S. Yu, Robert Abel, 2020, Journal of chemical theory and computation.

A displaced-solvent functional analysis of model hydrophobic enclosures.

Robert Abel, Lingle Wang, Richard A Friesner, 2010, Journal of chemical theory and computation.

Dewetting transitions in protein cavities

B. Berne, R. Friesner, Lan Hua, 2010, Proteins.

Schrödinger-ANI: An Eight-Element Neural Network Interaction Potential with Greatly Expanded Coverage of Druglike Chemical Space pdf

Robert Abel, Yutong Zhao, James M. Stevenson, 2019, ArXiv.

Molecular Structure Extraction From Documents Using Deep Learning

Robert Abel, Kyle Marshall, Joshua Staker, 2018, J. Chem. Inf. Model..

Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein–Protein Interfaces

R. Friesner, Robert Abel, Lingle Wang, 2019, Journal of molecular biology.

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

Robert Abel, Lingle Wang, Kevin Hauser, 2017, Communications Biology.

From computer-aided drug discovery to computer-driven drug discovery.

Robert Abel, Sathesh Bhat, Karen Akinsanya, 2021, Drug discovery today. Technologies.

Correction to "Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States".

Haoyu S. Yu, Robert Abel, Lingle Wang, 2019, Journal of chemical theory and computation.

WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking.

Matthew P. Repasky, R. Friesner, R. Murphy, 2016, Journal of medicinal chemistry.

Contribution of Explicit Solvent Effects to the Binding Affinity of Small‐Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

Noeris K. Salam, R. Friesner, W. Sherman, 2011, ChemMedChem.

Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

Daniel J. Sindhikara, Haoyu S. Yu, Robert Abel, 2017, Journal of chemical theory and computation.

Sensitivity in binding free energies due to protein reorganization

D. Mobley, Robert Abel, Lingle Wang, 2016, bioRxiv.

Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid.

Robert Abel, Lingle Wang, Richard A Friesner, 2009, Journal of chemical theory and computation.

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding.

Daniel J. Sindhikara, S. L. Dixon, Matthew J. Grisewood, 2021, Journal of chemical theory and computation.

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

R. Friesner, Kai Zhu, Suwen Zhao, 2011, Proteins.

Contributions of water transfer energy to protein‐ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

W. Sherman, Robert Abel, R. Pearlstein, 2013, Proteins.

F reticulocyte response in sickle cell anemia treated with recombinant human erythropoietin: a double-blind study.

G. Stamatoyannopoulos, R. Nagel, Robert Abel, 1993, Blood.

Preoperative assessment for cardiac surgery

Robert Abel, C. Evans, 2009 .