The MolSSI QCArchive project: An open‐source platform to compute, organize, and share quantum chemistry data

[1]  Shantenu Jha,et al.  Building Blocks for Workflow System Middleware , 2018, 2018 18th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID).

[2]  Matthew Rocklin,et al.  Dask: Parallel Computation with Blocked algorithms and Task Scheduling , 2015, SciPy.

[3]  Wei Chen,et al.  FireWorks: a dynamic workflow system designed for high‐throughput applications , 2015, Concurr. Comput. Pract. Exp..

[4]  G. Hunault,et al.  Dataset’s chemical diversity limits the generalizability of machine learning predictions , 2019, Journal of Cheminformatics.

[5]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[6]  Kristin A. Persson,et al.  Commentary: The Materials Project: A materials genome approach to accelerating materials innovation , 2013 .

[7]  Roberto Peverati,et al.  ACCDB: A collection of chemistry databases for broad computational purposes , 2018, J. Comput. Chem..

[8]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[9]  Claudia Draxl,et al.  NOMAD: The FAIR concept for big data-driven materials science , 2018, MRS Bulletin.

[10]  David L. Mobley,et al.  Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1 , 2018, bioRxiv.

[11]  Ian Foster,et al.  Parsl: Pervasive Parallel Programming in Python , 2019, HPDC.

[12]  Alexandre Tkatchenko,et al.  Quantum-chemical insights from deep tensor neural networks , 2016, Nature Communications.

[13]  Pavlo O. Dral,et al.  Quantum chemistry structures and properties of 134 kilo molecules , 2014, Scientific Data.

[14]  Lori A Burns,et al.  Basis set convergence of the coupled-cluster correction, δ(MP2)(CCSD(T)): best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases. , 2011, The Journal of chemical physics.

[15]  Daniel G A Smith,et al.  Psi4 1.4: Open-source software for high-throughput quantum chemistry. , 2020, The Journal of chemical physics.

[16]  Lee-Ping Wang,et al.  Geometry optimization made simple with translation and rotation coordinates. , 2016, The Journal of chemical physics.

[17]  Vijay S. Pande,et al.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics , 2016, bioRxiv.

[18]  Wes McKinney,et al.  Data Structures for Statistical Computing in Python , 2010, SciPy.

[19]  Martin Schütz,et al.  Molpro: a general‐purpose quantum chemistry program package , 2012 .

[20]  J S Smith,et al.  ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost , 2016, Chemical science.

[21]  Alexander D. MacKerell,et al.  The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. , 2017, The Journal of chemical physics.

[22]  Adrian E. Roitberg,et al.  Less is more: sampling chemical space with active learning , 2018, The Journal of chemical physics.

[23]  T. Straatsma,et al.  NWChem: Past, present, and future. , 2020, The Journal of chemical physics.

[24]  Gregory J O Beran,et al.  Accurate Noncovalent Interactions via Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory. , 2018, Journal of chemical theory and computation.

[25]  Jirí Cerný,et al.  Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. , 2006, Physical chemistry chemical physics : PCCP.

[26]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics. , 2009, Journal of chemical theory and computation.

[27]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[28]  Amir Karton,et al.  Performance of ab initio and density functional methods for conformational equilibria of C(n)H(2n+2) alkane isomers (n = 4-8). , 2009, The journal of physical chemistry. A.

[29]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[30]  Evan Bolton,et al.  PubChem 2019 update: improved access to chemical data , 2018, Nucleic Acids Res..

[31]  Maho Nakata,et al.  PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry , 2017, J. Chem. Inf. Model..

[32]  Donald G Truhlar,et al.  Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods. , 2005, The journal of physical chemistry. A.

[33]  Andy B. Yoo,et al.  Approved for Public Release; Further Dissemination Unlimited X-ray Pulse Compression Using Strained Crystals X-ray Pulse Compression Using Strained Crystals , 2002 .

[34]  Alán Aspuru-Guzik,et al.  Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , 2014, Molecular Physics.

[35]  Alexander S. Rose,et al.  NGLview–interactive molecular graphics for Jupyter notebooks , 2018, Bioinform..

[36]  Kristian S. Thygesen,et al.  Making the most of materials computations , 2016, Science.

[37]  E. Nestler,et al.  Granulocyte-colony stimulating factor controls neural and behavioral plasticity in response to cocaine , 2018, Nature Communications.

[38]  Olexandr Isayev,et al.  ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules , 2017, Scientific Data.

[39]  Xiao Wang,et al.  Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. , 2017, Journal of chemical theory and computation.

[40]  Tim Head,et al.  Binder 2.0 - Reproducible, interactive, sharable environments for science at scale , 2018, SciPy.

[41]  C David Sherrill,et al.  Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. , 2011, Journal of chemical theory and computation.

[42]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[43]  Nancy Wilkins-Diehr,et al.  The Science Gateways Community Institute at Two Years , 2018, PEARC.

[44]  Daniel G A Smith,et al.  Driving torsion scans with wavefront propagation. , 2020, The Journal of chemical physics.

[45]  et al.,et al.  Jupyter Notebooks - a publishing format for reproducible computational workflows , 2016, ELPUB.

[46]  Michael W. Schmidt,et al.  Recent developments in the general atomic and molecular electronic structure system. , 2020, The Journal of chemical physics.