Literature DB >> 30441927

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

Anna Krylov1, Theresa L Windus2, Taylor Barnes3, Eliseo Marin-Rimoldi3, Jessica A Nash3, Benjamin Pritchard3, Daniel G A Smith3, Doaa Altarawy3, Paul Saxe3, Cecilia Clementi4, T Daniel Crawford5, Robert J Harrison6, Shantenu Jha7, Vijay S Pande8, Teresa Head-Gordon9.   

Abstract

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.

Entities:  

Year:  2018        PMID: 30441927     DOI: 10.1063/1.5052551

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Authors:  Daniel G A Smith; Lori A Burns; Andrew C Simmonett; Robert M Parrish; Matthew C Schieber; Raimondas Galvelis; Peter Kraus; Holger Kruse; Roberto Di Remigio; Asem Alenaizan; Andrew M James; Susi Lehtola; Jonathon P Misiewicz; Maximilian Scheurer; Robert A Shaw; Jeffrey B Schriber; Yi Xie; Zachary L Glick; Dominic A Sirianni; Joseph Senan O'Brien; Jonathan M Waldrop; Ashutosh Kumar; Edward G Hohenstein; Benjamin P Pritchard; Bernard R Brooks; Henry F Schaefer; Alexander Yu Sokolov; Konrad Patkowski; A Eugene DePrince; Uğur Bozkaya; Rollin A King; Francesco A Evangelista; Justin M Turney; T Daniel Crawford; C David Sherrill
Journal:  J Chem Phys       Date:  2020-05-14       Impact factor: 3.488

2.  BCL::Mol2D-a robust atom environment descriptor for QSAR modeling and lead optimization.

Authors:  Oanh Vu; Jeffrey Mendenhall; Doaa Altarawy; Jens Meiler
Journal:  J Comput Aided Mol Des       Date:  2019-04-06       Impact factor: 3.686

3.  Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Authors:  Daniel G A Smith; Annabelle T Lolinco; Zachary L Glick; Jiyoung Lee; Asem Alenaizan; Taylor A Barnes; Carlos H Borca; Roberto Di Remigio; David L Dotson; Sebastian Ehlert; Alexander G Heide; Michael F Herbst; Jan Hermann; Colton B Hicks; Joshua T Horton; Adrian G Hurtado; Peter Kraus; Holger Kruse; Sebastian J R Lee; Jonathon P Misiewicz; Levi N Naden; Farhad Ramezanghorbani; Maximilian Scheurer; Jeffrey B Schriber; Andrew C Simmonett; Johannes Steinmetzer; Jeffrey R Wagner; Logan Ward; Matthew Welborn; Doaa Altarawy; Jamshed Anwar; John D Chodera; Andreas Dreuw; Heather J Kulik; Fang Liu; Todd J Martínez; Devin A Matthews; Henry F Schaefer; Jiří Šponer; Justin M Turney; Lee-Ping Wang; Nuwan De Silva; Rollin A King; John F Stanton; Mark S Gordon; Theresa L Windus; C David Sherrill; Lori A Burns
Journal:  J Chem Phys       Date:  2021-11-28       Impact factor: 3.488

4.  Molecular latent space simulators.

Authors:  Hythem Sidky; Wei Chen; Andrew L Ferguson
Journal:  Chem Sci       Date:  2020-08-26       Impact factor: 9.825

Review 5.  Frontiers in Multiscale Modeling of Photoreceptor Proteins.

Authors:  Maria-Andrea Mroginski; Suliman Adam; Gil S Amoyal; Avishai Barnoy; Ana-Nicoleta Bondar; Veniamin A Borin; Jonathan R Church; Tatiana Domratcheva; Bernd Ensing; Francesca Fanelli; Nicolas Ferré; Ofer Filiba; Laura Pedraza-González; Ronald González; Cristina E González-Espinoza; Rajiv K Kar; Lukas Kemmler; Seung Soo Kim; Jacob Kongsted; Anna I Krylov; Yigal Lahav; Michalis Lazaratos; Qays NasserEddin; Isabelle Navizet; Alexander Nemukhin; Massimo Olivucci; Jógvan Magnus Haugaard Olsen; Alberto Pérez de Alba Ortíz; Elisa Pieri; Aditya G Rao; Young Min Rhee; Niccolò Ricardi; Saumik Sen; Ilia A Solov'yov; Luca De Vico; Tomasz A Wesolowski; Christian Wiebeler; Xuchun Yang; Igor Schapiro
Journal:  Photochem Photobiol       Date:  2021-02-13       Impact factor: 3.521

6.  A deep neural network model for packing density predictions and its application in the study of 1.5 million organic molecules.

Authors:  Mohammad Atif Faiz Afzal; Aditya Sonpal; Mojtaba Haghighatlari; Andrew J Schultz; Johannes Hachmann
Journal:  Chem Sci       Date:  2019-07-09       Impact factor: 9.825

7.  Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.

Authors:  Miłosz Wieczór; Vito Genna; Juan Aranda; Rosa M Badia; Josep Lluís Gelpí; Vytautas Gapsys; Bert L de Groot; Erik Lindahl; Martí Municoy; Adam Hospital; Modesto Orozco
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2022-05-30
  7 in total

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