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Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies

Journal of chemical information and modeling, 2020-11, Vol.60 (11), p.5331-5339

2020

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Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

The Journal of chemical physics, 2014-12, Vol.141 (21), p.214106-214106

2014

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Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Chemical science (Cambridge), 2020-03, Vol.11 (1), p.267-268

2020

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Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2124-2130

2021

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Self-organized emergence of folded protein-like network structures from geometric constraints

PloS one, 2020-02, Vol.15 (2), p.e0229230-e0229230

2020

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Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors

PloS one, 2019-03, Vol.14 (3), p.e0213217-e0213217

2019

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Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer

Viruses, 2023-03, Vol.15 (3), p.697

2023

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Assessment of Binding Affinity via Alchemical Free-Energy Calculations

Journal of chemical information and modeling, 2020-06, Vol.60 (6), p.3120-3130

2020

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Variational Approach to Molecular Kinetics

Journal of chemical theory and computation, 2014-04, Vol.10 (4), p.1739-1752

2014

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Digital skills in chemical education

Nature chemistry, 2024-09, Vol.16 (9), p.1383-1384

2024

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Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

Journal of computer-aided molecular design, 2017, Vol.31 (1), p.61-70

2017

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Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs

The Journal of chemical physics, 2024-05, Vol.160 (20)

2024

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Elucidation of Nonadditive Effects in Protein–Ligand Binding Energies: Thrombin as a Case Study

The journal of physical chemistry. B, 2016-06, Vol.120 (24), p.5340-5350

2016

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Dynamic Profiling of β‑Coronavirus 3CL Mpro Protease Ligand-Binding Sites

Journal of chemical information and modeling, 2021-06, Vol.61 (6), p.3058-3073

2021

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Blinded predictions of distribution coefficients in the SAMPL5 challenge

Journal of computer-aided molecular design, 2016-11, Vol.30 (11), p.1101-1114

2016

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Shedding Light on the Dock–Lock Mechanism in Amyloid Fibril Growth Using Markov State Models

The journal of physical chemistry letters, 2015-03, Vol.6 (6), p.1076-1081

2015

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xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States

Physical review. X, 2014-10, Vol.4 (4), p.041018, Article 041018

2014

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Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

Journal of computer-aided molecular design, 2018-01, Vol.32 (1), p.199-210

2018

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SILVR: Guided Diffusion for Molecule Generation

Journal of chemical information and modeling, 2023-10, Vol.63 (19), p.5996-6005

2023

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Markov State Models: To Optimize or Not to Optimize

Journal of chemical theory and computation, 2024-01, Vol.20 (2), p.977-988

2024

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From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction

Journal of chemical information and modeling, 2024-04, Vol.64 (7), p.2496-2507

2024

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Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction

Journal of chemical information and modeling, 2024-03, Vol.64 (6), p.1955-1965

2024

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EMMA: A Software Package for Markov Model Building and Analysis

Journal of chemical theory and computation, 2012-07, Vol.8 (7), p.2223-2238

2012

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What geometrically constrained models can tell us about real-world protein contact maps

Physical biology, 2023-07, Vol.20 (4), p.46004

2023

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Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins

Biophysical reviews, 2016, Vol.8 (4), p.429-439

2016

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Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations

Self-organized emergence of folded protein-like network structures from geometric constraints

Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors

Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer

Assessment of Binding Affinity via Alchemical Free-Energy Calculations

Variational Approach to Molecular Kinetics

Digital skills in chemical education

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs

Elucidation of Nonadditive Effects in Protein–Ligand Binding Energies: Thrombin as a Case Study

Dynamic Profiling of β‑Coronavirus 3CL Mpro Protease Ligand-Binding Sites

Blinded predictions of distribution coefficients in the SAMPL5 challenge

Shedding Light on the Dock–Lock Mechanism in Amyloid Fibril Growth Using Markov State Models

xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

SILVR: Guided Diffusion for Molecule Generation

Markov State Models: To Optimize or Not to Optimize

From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction

Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction

EMMA: A Software Package for Markov Model Building and Analysis

What geometrically constrained models can tell us about real-world protein contact maps

Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins

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