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SUMMARY:Using Crystal for computational chemistry and drug design - Mauric
 io Bedoya
DTSTART;TZID=Europe/Berlin:20231024T143000
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DTSTAMP:20260812T201611Z
UID:pretalx-crystalconf-2023-MRJD3C@pretalx.com
DESCRIPTION:Computational chemistry is a rapidly growing field that uses c
 omputers for running simulations to study the properties of molecules and 
 materials. Computer-aided drug design (CADD) is a branch of computational 
 chemistry that uses molecular modelling and simulation to help understand 
 and design new drugs.\n\nScientists often need to deal with tons of data (
 big data) generated by specialized software\, which needs to be processed 
 to extract relevant information. We have developed a modern computational 
 chemistry library\, termed `chem.cr`\, for data manipulation and analysis 
 using the Crystal language.\n\n`chem.cr` aims to be both fast and easy to 
 use\, and it currently provides several features:\n\n* Hierarchical object
 -oriented access to molecular structure\n* Iterator-based file reading of 
 several formats (PDB\, Mol2\, etc)\n* Topology detection\n* Spatial measur
 ements\n* Volumetric data\n* Type safety\n* Fast performance\, rivaling or
  even surpassing other libraries built with Python/C/C++\n\n`chem.cr` has 
 already been used to develop and publish a new algorithm for protein struc
 ture ([Adasme-Carreño et al.\, 2021](https://doi.org/10.1021/acs.jcim.0c0
 1343))\, and we're developing new protocols for molecular docking and free
  energy calculations (`Femdock` and `Moltiverse`) that are crucial for CAD
 D.\n\n* `Femdock` helps to sample the possible orientations of a drug with
 in a protein binding site using a genetic algorithm\, like other molecular
  docking approaches\, but thanks to the Crystal language\, the code is cle
 arer and easier to understand and modify.\n* `Moltiverse` is used to gener
 ate molecular conformers of the drug using enhanced sampling methods\, tha
 t directly support the exploration performed by Femdock.\n\nWe hope that t
 his new library and protocols will help scientists to develop new/better t
 ools that accelerate drug discovery and the study of molecular structure.\
 n\n**References**\n\n* Adasme-Carreño\, F.\, Caballero\, J.\, & Ireta\, J
 . (2021). PSIQUE: Protein Secondary Structure Identification on the Basis 
 of Quaternions and Electronic Structure Calculations. Journal of Chemical 
 Information and Modeling\, 61(4)\, 1789–1800. https://doi.org/10.1021/ac
 s.jcim.0c01343
LOCATION:Main
URL:https://pretalx.com/crystalconf-2023/talk/MRJD3C/
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