Assessing conformer energies using electronic structure and machine learning methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Polarisable force fields: what do they add in biomolecular simulations?

(2020) VS Sandeep Inakollu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Energy windows for computed compound conformers: covering artefacts or truly large reorganization energies?

(2019) Nicolas Foloppe et al.   Future Medicinal Chemistry

PEPCONF, a diverse data set of peptide conformational energies

(2019) Viki Kumar Prasad et al.   Scientific Data

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

(2019) Katarina Roos et al.   Journal of Chemical Theory and Computation

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

(2019) Zhifeng Jing et al.   Annual Review of Biophysics

A generally applicable atomic-charge dependent London dispersion correction

(2019) Eike Caldeweyher et al.   JOURNAL OF CHEMICAL PHYSICS

AMOEBA+ Classical Potential for Modeling Molecular Interactions

(2019) Chengwen Liu et al.   Journal of Chemical Theory and Computation

Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s

(2019) Joel Wahl et al.   Journal of Cheminformatics

Method for Predicting Dipole Moments of Complex Molecules for Use in Thermophysical Property Estimation

(2019) Minh Nguyen Vo et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations

(2019) Brajesh K. Rai et al.   Journal of Chemical Information and Modeling

Advances and challenges in modeling solvated reaction mechanisms for renewable fuels and chemicals

(2019) Yasemin Basdogan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

BAND NN: A Deep Learning Framework for Energy Prediction and Geometry Optimization of Organic Small Molecules

(2019) Siddhartha Laghuvarapu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comprehensive Benchmark Results for the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)) for Closed- and Open-Shell Systems

(2019) Dimitrios G. Liakos et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Exploring conformational preferences of alanine tetrapeptide by CCSD(T), MP2, and dispersion-corrected DFT methods

(2018) Young Kee Kang et al.   CHEMICAL PHYSICS LETTERS

B97-3c: A revised low-cost variant of the B97-D density functional method

(2018) Jan Gerit Brandenburg et al.   JOURNAL OF CHEMICAL PHYSICS

Communication: An improved linear scaling perturbative triples correction for the domain based local pair-natural orbital based singles and doubles coupled cluster method [DLPNO-CCSD(T)]

(2018) Yang Guo et al.   JOURNAL OF CHEMICAL PHYSICS

Less is more: Sampling chemical space with active learning

(2018) Justin S. Smith et al.   JOURNAL OF CHEMICAL PHYSICS

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

(2018) Changsheng Zhang et al.   Journal of Chemical Theory and Computation

Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set

(2018) Jan Řezáč et al.   Journal of Chemical Theory and Computation

A paramedic treatment for modeling explicitly solvated chemical reaction mechanisms

(2018) Yasemin Basdogan et al.   Chemical Science

A Robust and Cost‐Efficient Scheme for Accurate Conformational Energies of Organic Molecules

(2018) Dmitry I. Sharapa et al.   CHEMPHYSCHEM

Toward Learned Chemical Perception of Force Field Typing Rules

(2018) Camila Zanette et al.   Journal of Chemical Theory and Computation

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

(2018) David van der Spoel et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A sobering assessment of small-molecule force field methods for low energy conformer predictions

(2017) Ilana Y. Kanal et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

(2017) Federico Zahariev et al.   Journal of Chemical Information and Modeling

Conformation Generation: The State of the Art

(2017) Paul C. D. Hawkins   Journal of Chemical Information and Modeling

Extension of the D3 dispersion coefficient model

(2017) Eike Caldeweyher et al.   JOURNAL OF CHEMICAL PHYSICS

Assessing DFT-D3 Damping Functions Across Widely Used Density Functionals: Can We Do Better?

(2017) Jonathon Witte et al.   Journal of Chemical Theory and Computation

Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error

(2017) Felix A. Faber et al.   Journal of Chemical Theory and Computation

A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)

(2017) Stefan Grimme et al.   Journal of Chemical Theory and Computation

Efficient DLPNO–CCSD(T)-Based Estimation of Formation Enthalpies for C-, H-, O-, and N-Containing Closed-Shell Compounds Validated Against Critically Evaluated Experimental Data

(2017) Eugene Paulechka et al.   JOURNAL OF PHYSICAL CHEMISTRY A

An optimized charge penetration model for use with the AMOEBA force field

(2017) Joshua A. Rackers et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2017) J. S. Smith et al.   Chemical Science

Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

(2016) Mohammad M. Ghahremanpour et al.   JOURNAL OF CHEMICAL PHYSICS

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

(2016) Bing Huang et al.   JOURNAL OF CHEMICAL PHYSICS

Consistent structures and interactions by density functional theory with small atomic orbital basis sets

(2015) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods

(2015) Manoj K. Kesharwani et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory

(2015) Dimitrios G. Liakos et al.   Journal of Chemical Theory and Computation

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

(2015) Kyle A. Beauchamp et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

(2015) Katja Hansen et al.   Journal of Physical Chemistry Letters

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations

(2014) Stefan Grimme   Journal of Chemical Theory and Computation

Comprehensive Analysis of Energy Minima of the 20 Natural Amino Acids

(2014) Yongna Yuan et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small Ligands

(2014) Jordi Juárez-Jiménez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural and Conformational Dispersion in the Rational Design of Conjugated Polymers

(2014) Nicholas E. Jackson et al.   MACROMOLECULES

Quantum chemistry structures and properties of 134 kilo molecules

(2014) Raghunathan Ramakrishnan et al.   Scientific Data

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies

(2013) Katja Hansen et al.   Journal of Chemical Theory and Computation

What Can We Learn about Dispersion from the Conformer Surface of n-Pentane?

(2013) Jan M. L. Martin   JOURNAL OF PHYSICAL CHEMISTRY A

Controlling Conformations of Conjugated Polymers and Small Molecules: The Role of Nonbonding Interactions

(2013) Nicholas E. Jackson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Freely Available Conformer Generation Methods: How Good Are They?

(2012) Jean-Paul Ebejer et al.   Journal of Chemical Information and Modeling

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

(2012) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

(2012) Matthias Rupp et al.   PHYSICAL REVIEW LETTERS

Computational Prediction of 1H and 13C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry

(2011) Michael W. Lodewyk et al.   CHEMICAL REVIEWS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Density functional theory with London dispersion corrections

(2011) Stefan Grimme   Wiley Interdisciplinary Reviews-Computational Molecular Science

The ORCA program system

(2011) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Efficient Structure Optimization with Second-Order Many-Body Perturbation Theory: The RIJCOSX-MP2 Method

(2010) Simone Kossmann et al.   Journal of Chemical Theory and Computation

ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces

(2010) Benjamin Waldher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Performance of Ab Initio and Density Functional Methods for Conformational Equilibria ofCnH2n+2Alkane Isomers (n= 4−8)†

(2009) David Gruzman et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Dispersion interactions in density-functional theory

(2009) Erin R. Johnson et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

(2008) Noel M O'Boyle et al.   Chemistry Central Journal

Torsional Barriers and Equilibrium Angle of Biphenyl: Reconciling Theory with Experiment

(2008) Mikael P. Johansson et al.   Journal of Chemical Theory and Computation

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

(2008) Jeng-Da Chai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

cclib: A library for package-independent computational chemistry algorithms

(2007) Noel M. O'boyle et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY