Publications

Preprints

1
Energetics of a protein disorder-order transition in small molecule recognition

Journal Publications

57
Implementation of the QUBE Force Field for High-Throughput Alchemical Free Energy Calculations
56
Designing Stapled Peptides to Inhibit Protein-Protein Interactions: An Analysis of Successes in a Rapidly Changing Field
55
Best Practices for Alchemical Free Energy Calculations
54
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes
53
A hybrid Alchemical Free Energy/Machine Learning Methodology for the Computation of Hydration Free Energies
52
Assessment of Binding Affinity via Alchemical Free Energy Calculations
51
Investigating Cryptic Binding Sites by Molecular Dynamics Simulations
50
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations
49
Dynamic design: manipulation of millisecond timescale motions on the energy landscape of Cyclophilin A
48
BioSimSpace: An interoperable Python framework for biomolecular simulation
47
Allosteric effects in a catalytically impaired variant of the enzyme Cyclophilin A are unrelated to millisecond time scale motions
46
Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
45
A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors
44
Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software
43
Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity
42
Blinded Predictions of Standard Binding Free Energies: Lessons Learned from the SAMPL6 Challenge
41
Metabolism and hydrophilicity of the polarised ‘Janus face’ all-cis tetrafluorocyclohexyl ring, a candidate motif for drug discovery
40
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
39
Pushing The Limits Of Detection Of Weak Binding Using Fragment Based Drug Discovery: Identification Of New Cyclophilin Binders
38
Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory
37
Blinded predictions of distribution coefficients in the SAMPL5 challenge
36
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge
35
Blinded predictions of binding modes and energies of HSP90-alpha ligands for the 2015 D3R Grand Challenge
34
Elucidation of Non-Additive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study
33
Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2
32
FESetup: Automating Setup for Alchemical Free Energy Simulations
31
Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate complexes
30
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2
29
A Collective Variable for the Rapid Exploration of Protein Druggability
28
Evaluation of Water Displacement Energetics in Protein Binding Sites with Grid Cell Theory
27
Evaluation of Host/Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory
26
25
24
Current and Emerging Opportunities for Molecular Simulations in Structure-Based Drug Design
23
Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1

Patents

3
2
1
East Chem
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