ArticlePloS one2012
FragIt: a tool to prepare input files for fragment based quantum chemical calculations.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 52 citations in OpenAlex.
- Comprehensive Comparison of Molecular Fragmentation Schemes for Proteins.Journal of chemical theory and computation · 2026Article
- Visualization of Properties in the Fragment Molecular Orbital Method Using Facio.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Inhibitor ranking through QM based chelation calculations for virtual screening of HIV-1 RNase H inhibition.PloS one · 2014Article
- Article
- Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.PloS one · 2014Article
- Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.PloS one · 2013Article
- Article
- Fragme∩t: An Open-Source Framework for Multiscale Quantum Chemistry Based on Fragmentation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available to support these methods and help to set up reasonable input files which will lower the barrier of entry for usage by non-experts. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files. We present a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. FragIt uses the SMARTS language to locate chemically appropriate fragments in large structures and is applicable to fragmentation of any molecular system given suitable SMARTS patterns. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to prepare input files for the Fragment Molecular Orbital method in the GAMESS program package, but can be extended to other computational methods easily.
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