Open source molecular modeling

Pirhadi, Somayeh; Sunseri, Jocelyn

doi:10.1016/j.jmgm.2016.07.008

Cited by 91 publications

(55 citation statements)

References 182 publications

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“…Open source software packages for molecular modelling and computational chemistry (Pirhadi, Sunseri & Koes, 2016) could be used for this purpose.…”

Section: Discussionmentioning

confidence: 99%

Determination of Prospective Chemistry Teachers’ Cognitive Structures and Misconceptions About Stereochemistry

Durmaz

2018

JETS

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The purpose of this study was to investigate the cognitive structures of chemistry teacher candidates about "stereochemistry". A case study research method, one of the qualitative research patterns, was used in the study and the sample of study involved 28 prospective chemistry teachers who had taken Organic Chemistry I and II courses at Education Faculty of a middle Anatolian university. For the data collection, stereochemistry concept inventory comprising of 20 questions was used. In the analysis of data, students' responses in SCI were categorized. The detailed analysis of the results indicated that chemistry teacher candidates had some misconceptions concerning stereochemistry parallel to the literature. Based on these observations, some suggestions were presented for improving students' foundational understanding about stereochemistry.

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“…Open source software packages for molecular modelling and computational chemistry (Pirhadi, Sunseri & Koes, 2016) could be used for this purpose.…”

Section: Discussionmentioning

confidence: 99%

Determination of Prospective Chemistry Teachers’ Cognitive Structures and Misconceptions About Stereochemistry

Durmaz

2018

JETS

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“…In parallel, JavaScript interpreters in web browsers have improved dramatically, and now enable use of graphics applications directly within a web browser. There are a growing number of efforts aimed at developing JavaScript/WebGL based 3D viewers (13). RCSB PDB has supported JSmol (JSmol: an open-source HTML5 viewer for chemical structures in 3D, http://wiki.jmol.org/index.php/JSmol) and PV (14) for some time, and recently added support for NGL.…”

Section: New Website Featuresmentioning

confidence: 99%

OUP accepted manuscript

Rose

Prlić

Altunkaya

et al. 2016

Nucleic Acids Research

535

233

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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

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“…The Made Smarter Review of 2017 identified that adopting digital prediction in industrial workflows could streamline economical and material overheads in manufacturing. One barrier to the adoption of such technology can be the usability and the ease of understanding of the software developed , . Recent publications have highlighted promising workflows, where molecular modeling approaches appraise solution and particle chemistry of organic materials .…”

Section: Introductionmentioning

confidence: 99%

Computational Analysis of the Solid‐State and Solvation Properties of Carbamazepine in Relation to its Polymorphism

2020

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The solvent-dependent polymorphism of the active pharmaceutical ingredient (API) carbamazepine is interpreted from calculations of the solid-state and API-solvent intermolecular interactions. These simulations suggested that apolar solute-solute interactions could be disrupted by apolar solvents. In contrast, the polar solute-solute interactions were found to be easily disrupted by polar and protic solvents. This is consistent with experimental observations that the crystallization of the metastable form II is more dominant in apolar solvents. The Mercury program remains the gold standard in terms of usability; however, further expansion into more complex simulation techniques could make this package of even greater use in pharmaceutical manufacturing workflows.

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Open source molecular modeling

Cited by 91 publications

References 182 publications

Determination of Prospective Chemistry Teachers’ Cognitive Structures and Misconceptions About Stereochemistry

Determination of Prospective Chemistry Teachers’ Cognitive Structures and Misconceptions About Stereochemistry

OUP accepted manuscript

Computational Analysis of the Solid‐State and Solvation Properties of Carbamazepine in Relation to its Polymorphism

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