OpenScience / Software / Chemistry / Biochemistry

A package of Python modules that allows you to do metabolic modelling. Find ScrumPy at: http://mudshark.brookes.ac.uk/ScrumPy

XLOGP is a method which can calculate the logP value for an organic compound from its topological structure Find XLOGP at: http://mdl.ipc.pku.edu.cn/drug_design/work/xlogp.html

SCORE is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Find SCORE at: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure … Continue reading →

LigBuilder is a multiple-purposed program written for structure-based drug design procedure. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them Find LigBuilder at: http://mdl.ipc.pku.edu.cn/drug_design/work/ligbuilder.html

EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety … Continue reading →