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List of works by Adrian Roitberg

A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease.

scientific article published on 8 January 2018

A Fast Implementation of the Nudged Elastic Band Method in AMBER

A Multiscale Treatment of Angeli's Salt Decomposition

scientific article published on 01 January 2009

A QM/MM free energy study of the oxidation mechanism of dihydroorotate dehydrogenase (class 1A) from Lactococcus lactis

scientific article published on 20 January 2015

A versatile AMBER-Gaussian QM/MM interface through PUPIL.

scientific article

AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing

scientific article published on 20 September 2013

AM1 parameters for the prediction of 1H and 13C NMR chemical shifts in proteins

scientific article published on 01 October 2009

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules.

scientific article published on 19 December 2017

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost.

scientific article

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

scientific article (publication date: September 2002)

Analysis of state-specific vibrations coupled to the unidirectional energy transfer in conjugated dendrimers

scientific article

Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.

scientific article published on December 2009

Applicability of fluorescence-based sensors to the determination of kinetic parameters for O₂ in oxygenases

scientific article

Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning ⬇️

scientific article published on 01 July 2019

Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning

Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.

scientific article

Axially Chiral Cannabinols: A New Platform for Cannabinoid-Inspired Drug Discovery

scientific article published on 15 February 2020

Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules

scientific article published on 28 April 2009

Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs

scientific article published on 29 August 2014

Cation-Dependent Conformations in 25-Hydroxyvitamin D3-Cation Adducts Measured by Ion Mobility-Mass Spectrometry and Theoretical Modeling

scientific article published on 22 May 2018

Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions

scientific article published on 6 June 2016

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics.

scientific article published on 13 June 2018

Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation"

scientific article published on 08 May 2012

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

scientific article (publication date: 15 November 2006)

Computational studies of ammonia channel function in glutamine 5'-phosphoribosylpyrophosphate amidotransferase

scientific article published in December 2009

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

scientific article published on September 2011

Conformational disorder in energy transfer: beyond Förster theory.

scientific article published on 8 May 2013

Conjugated polyelectrolyte dendrimers: aggregation, photophysics, and amplified quenching.

scientific article published on 17 October 2012

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

scientific article published on 05 February 2014

Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

scientific article

Correction to "dynamics of energy transfer in a conjugated dendrimer driven by ultrafast localization of excitations".

scientific article published on 28 October 2015

Correction: QSAR without borders

scientific article published on 22 May 2020

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

scientific article

Crown complexation of protonated amino acids: influence on IRMPD spectra

scientific article

Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency

scientific article

Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: screening for novel inhibitor scaffolds

scientific article published on 16 August 2013

Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials

scientific article published on 12 January 2022

Discovering a Transferable Charge Assignment Model Using Machine Learning

scientific article published on 27 July 2018

Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations.

scientific article

Electronic Delocalization, Vibrational Dynamics, and Energy Transfer in Organic Chromophores.

scientific article published on 12 June 2017

Electronic Spectra of the Nanostar Dendrimer: Theory and Experiment

Energy Transfer in the Nanostar: The Role of Coulombic Coupling and Dynamics

scientific article published on 01 June 2005

Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and π-Stacking

scientific article published on 20 July 2015

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

scientific article published on 14 September 2012

Exchange Often and Properly in Replica Exchange Molecular Dynamics

scientific article published on 28 July 2010

Exchange frequency in replica exchange molecular dynamics

scientific article published on 01 January 2008

Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry

scientific article published on 2 December 2016

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems

scientific article published on 14 February 2020

Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation

scientific article published on 19 October 2020

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

scientific article published on 7 February 2020

Extending the applicability of the ANI deep learning molecular potential to Sulfur and Halogens

scientific article published on 16 June 2020

Fast Implementation of the Nudged Elastic Band Method in AMBER

scientific article published on 31 July 2019

Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem

scientific article

Folding and Dynamics Are Strongly pH-Dependent in a Psychrophile Frataxin

scientific article published on 27 August 2019

Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate.

scientific article published on 27 October 2011

Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase.

scientific article

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

scientific article published on 25 September 2018

Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules.

scientific article

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy ⬇️

scientific article published on August 2010

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package

scientific article published on 24 May 2007

Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study.

scientific article published on 19 June 2015

Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations

scientific article published on 6 February 2015

Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling

scientific article

Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1-3 mutant.

scientific article

Kinetics of internal-loop formation in polypeptide chains: a simulation study

scientific article published on 5 January 2007

Less is more: Sampling chemical space with active learning

scientific article published on 01 June 2018

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

scientific article

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

scientific article published on 16 August 2012

Modulation of catalytic function by differential plasticity of the active site: case study of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase

scientific article published on April 2009

Molecular and functional characterization of a juvenile hormone acid methyltransferase expressed in the corpora allata of mosquitoes

scientific article

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

scientific article

Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics

scientific article published on 18 January 2019

Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase

scientific article published in May 2005

NEXMD Software Package for Non-adiabatic Excited State Molecular Dynamics Simulations

scientific article published on 07 July 2020

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials

scientific article published on 10 February 2020

Nonadiabatic excited-state molecular dynamics modeling of photoinduced dynamics in conjugated molecules.

scientific article published on 10 January 2011

Nonadiabatic excited-state molecular dynamics: modeling photophysics in organic conjugated materials

scientific article published on 27 March 2014

Nonadiabatic excited-state molecular dynamics: numerical tests of convergence and parameters

scientific article published in February 2012

Nonadiabatic excited-state molecular dynamics: treatment of electronic decoherence.

scientific article published in June 2013

Nonadiabatic molecular dynamics simulations of the energy transfer between building blocks in a phenylene ethynylene dendrimer

scientific article published in July 2009

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

scientific article

Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning

scientific article published on 31 October 2013

Oxygen diffusion pathways in a cofactor-independent dioxygenase.

scientific article

Photoexcited Nonadiabatic Dynamics of Solvated Push-Pull π-Conjugated Oligomers with the NEXMD Software

scientific article published on 13 July 2018

Preliminary molecular dynamic simulations of the estrogen receptor alpha ligand binding domain from antagonist to apo.

scientific article published on June 2008

Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy

scientific article published on 05 September 2018

Proton transfer facilitated by ligand binding. An energetic analysis of the catalytic mechanism of Trypanosoma cruzi trans-sialidase.

scientific article

QSAR without borders

scientific article published on 01 May 2020

Rationalizing the pH-Activity Response for Escherichia Coli’s Glycinamide Ribonucleotidetransformylase Through Computational Methods

Rationalizing the pH-Activity Response of Escherichia Coli Glycinamide Ribonucleotide Transformylase Through Computational Methods

scientific article published on 04 May 2020

Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

scientific article published on 01 August 2018

Selective ring-rearrangement or ring-closing metathesis of bicyclo[3.2.1]octenes

scientific article published on 17 September 2020

Shishiodoshi unidirectional energy transfer mechanism in phenylene ethynylene dendrimers

scientific article

Signature of nonadiabatic coupling in excited-state vibrational modes.

scientific article published on 24 June 2014

Simulating temperature jumps for protein folding

scientific article

Simulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems.

scientific article

Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type

scientific article

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

scientific article published in November 2002

Steered molecular dynamic simulations reveal Marfan syndrome mutations disrupt fibrillin-1 cbEGF domain mechanosensitive calcium binding

scientific article published on 08 October 2020

Structural analysis of ligand binding and catalysis in chorismate lyase

scientific article

Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity

scientific article published on 18 November 2016

Structures of biomolecular ions in the gas phase probed by infrared light sources

scientific article

Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase.

scientific article

The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

scientific article published on 01 May 2020

The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation

scientific article published on 01 October 2006

The any particle molecular orbital/molecular mechanics approach

scientific article published on 16 September 2019

The generalized Boltzmann distribution is the only distribution in which the Gibbs-Shannon entropy equals the thermodynamic entropy

scientific article published on 01 July 2019

Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis

scientific article published on 9 December 2016

Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy, and electrochemistry

scientific article published on 06 May 2008

Theoretical studies of short polyproline systems: recalibration of a molecular ruler

scientific article published on 01 April 2009

Theoretical study of the isomerization mechanism of azobenzene and disubstituted azobenzene derivatives

scientific article published on 01 July 2006

TorchANI: A Free and Open Source PyTorch Based Deep Learning Implementation of the ANI Neural Network Potentials

scientific article published on 22 June 2020

Total Synthesis of Axially-Chiral Cannabinols: A New Platform for Cannabinoid-Based Drug Discovery

Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks

scientific article published on 17 August 2018

Transforming Computational Drug Discovery with Machine Learning and AI

scientific article published on 08 October 2018

Trypanosoma cruzi trans-sialidase as a drug target against Chagas disease (American trypanosomiasis).

scientific article published on October 2013

Underlying thermodynamics of pH-dependent allostery.

scientific article

Unidirectional Energy Transfer in Conjugated Molecules: The Crucial Role of High-Frequency C≡C Bonds

Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study

scientific article

Wide-open flaps are key to urease activity

scientific article published on 11 June 2012

pH Effects and Cooperativity among Key Titratable Residues for <i>Escherichia coli</i> Glycinamide Ribonucleotide Transformylase

scientific article published in 2021

pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

scientific article published on 01 July 2019

pH-Dependent Conformational Changes Lead to a Highly Shifted p<i>K</i><sub>a</sub> for a Buried Glutamic Acid Mutant of SNase

scientific article published on 01 December 2020

pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4

scientific article

pH-REMD simulations indicate that the catalytic aspartates of HIV-1 protease exist primarily in a monoprotonated state

scientific article

pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

scientific article published on January 2009

pH-replica exchange molecular dynamics in proteins using a discrete protonation method

scientific article published on 17 July 2012

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