|
| 37200895 | A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. | | 2023 |
| 37645995 | LPATH: A semi-automated Python tool for clustering molecular pathways. | | 2023 |
| 37632831 | Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation. | Protein Sci | 2023 |
| 36647365 | #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. | Int J High Perform Comput Appl | 2023 |
| 35043623 | WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. | Journal of Chemical Theory and Computation | 2022 |
| 36320921 | Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics. | Chemical Science | 2022 |
| 35352936 | Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. | J Phys Chem A | 2022 |
| 34413500 | A glycan gate controls opening of the SARS-CoV-2 spike protein. | Nat Chem | 2021 |
| 33752378 | The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations. | Journal of Chemical Physics | 2021 |
| 33577732 | A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations. | Journal of Physical Chemistry A | 2021 |
| 33619492 | A glycan gate controls opening of the SARS-CoV-2 spike protein. | bioRxiv | 2021 |
| 34324338 | The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics. | Journal of Physical Chemistry B | 2021 |
| 34816263 | #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. | bioRxiv | 2021 |
| 35287464 | A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics. | J Chem Phys | 2020 |
| 30881664 | Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations. | Chemical Science | 2019 |
| 32395705 | A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. | | 2019 |
| 31042394 | Correction to "Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields". | J Phys Chem B | 2019 |
| 29523842 | Large enhancement of response times of a protein conformational switch by computational design. | Nature Communications | 2018 |
| 29490245 | Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. | Biophys J | 2018 |
| 27984811 | Path-sampling strategies for simulating rare events in biomolecular systems. | Current Opinion in Structural Biology | 2017 |
| 28992700 | Flexibility vs Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues. | Journal of Physical Chemistry B | 2017 |
| 29096508 | Links between the charge model and bonded parameter force constants in biomolecular force fields. | J Chem Phys | 2017 |
| 28301772 | Weighted Ensemble Simulation: Review of Methodology, Applications, and Software. | Annual Review of Biophysics | 2017 |
| 27532687 | Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide. | Journal of Physical Chemistry Letters | 2016 |
| 27399642 | Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. | J Chem Theory Comput | 2016 |
| 26131764 | Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. | Protein Science | 2016 |
| 26673903 | Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models. | Journal of Physical Chemistry B | 2016 |
| 26392815 | WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis. | Journal of Chemical Theory and Computation | 2015 |
| 24702709 | Evaluating the strength of salt bridges: a comparison of current biomolecular force fields. | J Phys Chem B | 2014 |
| 25246856 | Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories. | Journal of Chemical Theory and Computation | 2014 |
| 23116373 | The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state. | Biochemistry | 2012 |
| 22300130 | Effects of high temperature on desolvation costs of salt bridges across protein binding interfaces: similarities and differences between implicit and explicit solvent models. | Journal of Physical Chemistry B | 2012 |
| 21539773 | Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulations. | Biophysical Journal | 2011 |
| 26606365 | Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether. | Journal of Chemical Theory and Computation | 2011 |
| 21281591 | Molecular simulations of mutually exclusive folding in a two-domain protein switch. | Biophysical Journal | 2011 |
| 21528875 | Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations. | Journal of Physical Chemistry A | 2011 |
| 22098738 | Simulations of the alternating access mechanism of the sodium symporter Mhp1. | Biophysical Journal | 2011 |
| 20934381 | Reaching biological timescales with all-atom molecular dynamics simulations. | Current Opinion in Pharmacology | 2010 |
| 24920993 | Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models. | Journal of Physical Chemistry Letters | 2010 |
| 19168381 | Comparison of computational approaches for predicting the effects of missense mutations on p53 function. | Journal of Molecular Graphics and Modelling | 2009 |
| 19038264 | Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains. | Journal of Molecular Biology | 2009 |
| 16457841 | Kinetic computational alanine scanning: application to p53 oligomerization. | Journal of Molecular Biology | 2006 |
| 15588832 | Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. | Journal of Molecular Biology | 2005 |
| 12868101 | Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. | Journal of Computational Chemistry | 2003 |
| 11749542 | An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. | Journal of the American Chemical Society | 2001 |
| 11123888 | Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. | Acc Chem Res | 2000 |
| 10588705 | Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. | Proceedings of the National Academy of Sciences of the United States of America | 1999 |
| 10072689 | Selective, tight-binding inhibitors of integrin alpha4beta1 that inhibit allergic airway responses. | Journal of Medicinal Chemistry | 1999 |
| 9514276 | Computation of electrostatic complements to proteins: a case of charge stabilized binding. | Protein Science | 1998 |