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1

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

Gao, Xiang, Ramezanghorbani, Farhad, Isayev, Olexandr, Smith, Justin S., Roitberg, Adrian E.

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 1.53 MB

2020

2

Less is more: Sampling chemical space with active learning

Smith, Justin S., Nebgen, Ben, Lubbers, Nicholas, Isayev, Olexandr, Roitberg, Adrian E.

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

3

Transforming Computational Drug Discovery with Machine Learning and AI

Smith, Justin S., Roitberg, Adrian E., Isayev, Olexandr

Journal:

ACS Medicinal Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 1.75 MB

english, 2018

4

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

Nelson, Tammie R., White, Alexander J., Bjorgaard, Josiah A., Sifain, Andrew E., Zhang, Yu, Nebgen, Benjamin, Fernandez-Alberti, Sebastian, Mozyrsky, Dmitry, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Chemical Reviews

Year:

2020

File:

PDF, 19.43 MB

2020

5

Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem

Hopkins, Chad W., Roitberg, Adrian E.

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 2.24 MB

english, 2014

6

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

Devereux, Christian, Smith, Justin S., Davis, Kate K, Barros, Kipton, Zubatyuk, Roman, Isayev, Olexandr, Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 806 KB

2020

7

Nonadiabatic Excited-State Molecular Dynamics: Modeling Photophysics in Organic Conjugated Materials

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Accounts of Chemical Research

Year:

2014

Language:

english

File:

PDF, 3.29 MB

english, 2014

8

Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

Dissanayake, Thakshila, Swails, Jason M., Harris, Michael E., Roitberg, Adrian E., York, Darrin M.

Journal:

Year:

2015

Language:

english

File:

PDF, 925 KB

english, 2015

9

Molecular Wires: Charge Transport, Mechanisms, and Control

MARK A. RATNER, BILL DAVIS, MATHIEU KEMP, VLADIMIRO MUJICA, ADRIAN ROITBERG, SOPHIA YALIRAKI

Journal:

Annals of the New York Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 4.27 MB

english, 1998

10

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

Semenova, Evgeniya, Lahtigui, Ouidad, Scott, Sarah, Albritton, Matthew, Abboud, Khalil A, Ghiviriga, Ion, Roitberg, Adrian E., Grenning, Alexander

Journal:

Chemical Communications

Year:

2020

File:

PDF, 2.12 MB

2020

11

Nonadiabatic excited-state molecular dynamics: Treatment of electronic decoherence

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

12

Molecular Wire Interconnects: Chemical Structural Control, Resonant Tunneling and Length Dependence

Kemp, Mathieu, Mujica, Vladimiro, Roitberg, Adrian, Ratner, Mark A.

Journal:

Year:

1998

Language:

english

File:

PDF, 2.29 MB

english, 1998

13

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

Smith, Justin S., Nebgen, Benjamin T., Zubatyuk, Roman, Lubbers, Nicholas, Devereux, Christian, Barros, Kipton, Tretiak, Sergei, Isayev, Olexandr, Roitberg, Adrian E.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 1.19 MB

english, 2019

14

Nonadiabatic Excited-State Molecular Dynamics Modeling of Photoinduced Dynamics in Conjugated Molecules

Nelson, Tammie, Fernandez-Alberti, Sebastian, Chernyak, Vladimir, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 2.73 MB

english, 2011

15

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

Smith, Justin S., Isayev, Olexandr, Roitberg, Adrian E.

Journal:

Scientific Data

Year:

2017

Language:

english

File:

PDF, 1.38 MB

english, 2017

16

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

Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Nelson, Tammie, Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

17

Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Chemical Physics Letters

Year:

2013

Language:

english

File:

PDF, 775 KB

english, 2013

18

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

Miller III, Bill R, Roitberg, Adrian E

Journal:

Future Medicinal Chemistry

Year:

2013

Language:

english

File:

PDF, 3.10 MB

english, 2013

19

Signature of Nonadiabatic Coupling in Excited-State Vibrational Modes

Soler, Miguel A., Nelson, Tammie, Roitberg, Adrian E., Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Journal of Physical Chemistry A

Year:

2014

Language:

english

File:

PDF, 428 KB

english, 2014

20

Discovering a Transferable Charge Assignment Model Using Machine Learning

Sifain, Andrew E., Lubbers, Nicholas, Nebgen, Benjamin T., Smith, Justin S., Lokhov, Andrey Y., Isayev, Olexandr, Roitberg, Adrian E., Barros, Kipton, Tretiak, Sergei

Journal:

The Journal of Physical Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 907 KB

english, 2018

21

Structures of Biomolecular Ions in the Gas Phase Probed by Infrared Light Sources

Stedwell, Corey N., Galindo, Johan F., Roitberg, Adrian E., Polfer, Nicolas C.

Journal:

Annual Review of Analytical Chemistry

Year:

2013

Language:

english

File:

PDF, 1.06 MB

english, 2013

22

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

Miller, Bill R., McGee, T. Dwight, Swails, Jason M., Homeyer, Nadine, Gohlke, Holger, Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 951 KB

english, 2012

23

[Annual Reports in Computational Chemistry] Volume 1 || Chapter 8 Nonequilibrium Approaches to Free Energy Calculations

Roitberg, Adrian E.

Year:

2005

Language:

english

File:

PDF, 111 KB

english, 2005

24

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

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 2.21 MB

english, 2017

25

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective †

de M. Seabra, Gustavo, Walker, Ross C., Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 625 KB

english, 2009

26

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

Chouinard, Christopher D., Cruzeiro, Vinícius Wilian D., Beekman, Christopher R., Roitberg, Adrian E., Yost, Richard A.

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

27

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

Cruzeiro, Vinícius Wilian D., Amaral, Marcos S., Roitberg, Adrian E.

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 4.23 MB

english, 2018

28

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

Sarkar, Ankita, Gupta, Pancham Lal, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry B

Year:

2019

Language:

english

File:

PDF, 6.87 MB

english, 2019

29

Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study

González Lebrero, Mariano C., Bikiel, Damián E., Elola, M. Dolores, Estrin, Darı́o A., Roitberg, Adrian E.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 468 KB

english, 2002

30

Enzyme dynamics and catalysis in the mechanism of DNA polymerase

Adrian J. Mulholland, Adrian E. Roitberg, Iñaki Tuñón

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2012

Language:

english

File:

PDF, 187 KB

english, 2012

31

Structural study of a flexible active site loop in human indoleamine 2,3-dioxygenase and its functional implications

Alvarez, Lucia, Lewis Ballester, Ariel, Roitberg, Adrian E., Estrin, Dario A, Yeh, Syun-Ru, Marti, Marcelo A., Capece, Luciana

Journal:

Year:

2016

Language:

english

File:

PDF, 1.80 MB

english, 2016

32

Front Cover: Axially Chiral Cannabinols: A New Platform for CannabinoidâInspired Drug Discovery (ChemMedChem 9/2020)

Navaratne, Primali V., Wilkerson, Jenny L., Ranasinghe, Kavindri D., Semenova, Evgeniya, Felix, Jasmine S., Ghiviriga, Ion, Roitberg, Adrian, McMahon, Lance R., Grenning, Alexander J.

Journal:

Year:

2020

File:

PDF, 1.16 MB

2020

33

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

Jaime G. Mayoral, Marcela Nouzova, Michiyo Yoshiyama, Tetsuro Shinoda, Salvador Hernandez-Martinez, Elena Dolghih, Adrian G. Turjanski, Adrian E. Roitberg, Horacio Priestap, Mario Perez, Lucy Mackenzi

Journal:

Insect Biochemistry and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 415 KB

english, 2009

34

Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm

Ramírez, Claudia L., Zeida, Ari, Jara, Gabriel E., Roitberg, Adrián E., Martí, Marcelo A.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 608 KB

english, 2014

35

Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir

Roitberg, Adrian E., Okur, Asim, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 117 KB

english, 2007

36

Oxygen diffusion pathways in a cofactor-independent dioxygenase

Di Russo, Natali V., Condurso, Heather L., Li, Kunhua, Bruner, Steven D., Roitberg, Adrian E.

Journal:

Chemical Science

Year:

2015

Language:

english

File:

PDF, 1012 KB

english, 2015

37

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

Cruzeiro, Vinícius Wilian D., Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 1.45 MB

english, 2019

38

Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivatives

Crecca, Christina R., Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2006

Language:

english

File:

PDF, 1.34 MB

english, 2006

39

Simulating Temperature Jumps for Protein Folding

Kim, Seonah, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 388 KB

english, 2008

40

QSAR without borders

Muratov, Eugene N., Bajorath, JÃ¼rgen, Sheridan, Robert P., Tetko, Igor V., Filimonov, Dmitry, Poroikov, Vladimir, Oprea, Tudor I., Baskin, Igor I., Varnek, Alexandre, Roitberg, Adrian, Isayev, Olexan

Journal:

Chemical Society Reviews

Year:

2020

File:

PDF, 7.32 MB

2020

41

Foreword

Adrian Roitberg, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 23 KB

english, 2004

42

Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler †

Dolghih, Elena, Ortiz, Wilfredo, Kim, Seonah, Krueger, Brent P., Krause, Jeffrey L., Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 1.24 MB

english, 2009

43

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

Sanusi, Zainab K., Lawal, Monsurat M., Gupta, Pancham Lal., Govender, Thavendran, Baijnath, Sooraj, Naicker, Tricia, Maguire, Glenn E. M., Honarparvar, Bahareh, Roitberg, Adrian E., Kruger, Hendrik G.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2020

File:

PDF, 3.06 MB

2020

44

A versatile AMBER-Gaussian QM/MM interface through PUPIL

Juan Torras, Gustavo de M. Seabra, Erik Deumens, S. B. Trickey, Adrian E. Roitberg

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 468 KB

english, 2008

45

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

Luciana Capece, Mehrnoosh Arrar, Adrian E. Roitberg, Syun-Ru Yeh, Marcelo A. Marti, Dario A. Estrin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 596 KB

english, 2010

46

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

Fernandez-Alberti, S., Kleiman, Valeria D., Tretiak, S., Roitberg, Adrian E.

Journal:

The Journal of Physical Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 1.70 MB

english, 2010

47

Electronic Delocalization in Coordination Polymers Based on Bimetallic Carboxylates

Castro, María Ana, Roitberg, Adrián E., Cukiernik, Fabio D.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

48

Photosensitization of Single-Crystal ZnO by a Conjugated Polyelectrolyte Designed to Avoid Aggregation

Zhu, Xuzhi, Nepomnyashchii, Alexander B., Roitberg, Adrian E., Parkinson, B. A., Schanze, Kirk S.

Journal:

The Journal of Physical Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

49

Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans -Sialidase and Trypanosoma rangeli Sialidase †

Demir, Özlem, Roitberg, Adrian E.

Journal:

Year:

2009

Language:

english

File:

PDF, 3.51 MB

english, 2009

50

Free Energy Study of the Catalytic Mechanism of Trypanosoma cruzi trans -Sialidase. From the Michaelis Complex to the Covalent Intermediate

Pierdominici-Sottile, Gustavo, Horenstein, Nicole A., Roitberg, Adrian E.

Journal:

Year:

2011

Language:

english

File:

PDF, 2.20 MB

english, 2011

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