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High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
From 1965, the group began to collect published bibliographic, chemical and crystal structure data for all small molecules studied by X-ray or neutron diffraction. With the rapid developments in computing taking place at this time, this collection was encoded in electronic form and became known as the Cambridge Structural Database (CSD).
The SIRIUS software is developed by the group of Sebastian Böcker at the Friedrich Schiller University Jena, Germany and since 2019 together with Bright Giant GmbH.SIRIUS development started in 2009 as a software for identification of the molecular formula by decomposing high-resolution isotope patterns (also called MS1 data). [1]
ChemMantis, [14] the Chemistry Markup And Nomenclature Transformation Integrated System uses algorithms to identify and extract chemical names from documents and web pages and converts the chemical names to chemical structures using name-to-structure conversion algorithms and dictionary look-ups in the ChemSpider database. The result is an ...
Protein structure databases CATH database: Protein structure databases ModBase: Sali Lab, UCSF: database of comparative protein structure models Protein model databases SIMAP: database of protein similarities computed using FASTA: Protein model databases Swiss-model: server and repository for protein structure models Protein model databases AAindex
Edit, visualize and run simulations on various molecular systems. Spartan: MM QM: Proprietary [23] Standalone program [24] Visualize and edit biomolecules, extract bound ligands from PDB files for further computational analysis, full molecular mechanics and quantum chemical calculations package with streamlined graphical user interface. UCSF ...
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
Trivial names on the other hand abound with homonyms and synonyms and are therefore a bad choice as a defining database key. While physico-chemical descriptors like molecular weight, charge, solubility, etc. can mostly be computed directly based on the molecule's structure, pharmacological descriptors can be derived only indirectly using ...