RxnIP (FAQ)
Q: What is RxnIP?
A: RxnIP is an integrative platform to search, generalize, and annotate biochemical reactions.
Q: Functions provided in RxnIP?
A: Firstly, reaction database searching functions; seconldy, reaction generalizations by defining chemical transformation patterns; thirdly, EC number annotations to enzymatic reactions.
Q: Searching functions provided in RxnIP?
A: Three are three searching methods: partipating molecule, smart molecular fragment, and reaction similarity. Searching functions are listed at ReactDB
Q: Generalization functions provided in RxnIP?
A: More than 4000 reactions are generalized into 990 chemical transformation patterns. A mapping is built between EC numbers and chemical transformation patterns. Generalization functions are available at RxnPattern
Q: Automatic EC number annotation functions provided in RxnIP?
A: EC number assignment tool is developed to assign EC numbers to enzymatic reactions by using reaction difference fingerprints (RDF). EC number annotation functions are linked at ECAssigner
Q: Website (with example) to search reactions by participaing molecules?
A: At searching reactions by participating molecule (with example), users can retrieve reactions containg a specific molecule.
Q: Website (with example) to search reactions by molecular fragment?
A: At searching reactions by molecular fragment (with example), users can retrieve reactions containg a given molecular fragment.
Q: Website (with example) to search reactions by reaction similarity?
A: At searching reactions by reaction similarity (with example), users can retrieve reactions most similar to a input reaction.
Q: Website (with example) to get chemical transformation patterns?
A: At reaction pattern list , users can get intuitive patterns defined for EC numbers.
Q: Web server (with example) to extract chemical transformation patterns?
A: At RxnPatter , users can extract patterns for a input reaction.
Q: Website (with example) to search chemical transformation patterns by EC numbers?
A: At RxnPattern Searching for Given EC Numbers (with example), users can get patterns defined for a given EC number.
Q: Website (with example) to assign EC numbers to enzymatic reactions?
A: At EC Assignment (with example), users can get EC number annotation calculated for a given reaction.
Q: Where to contribute reactions to RxnIP?
A: At Reaction contribution, users can contribute reaction to RxnIP.
Q: How to draw molecule in RxnIP?
A: At Molecule input, users can draw molecular structures and get smiles string for a molecule.
Q: How to draw reaction in RxnIP?
A: At Reaction input, users can draw reactions and get smirks string for a reaction.
Q: How to get molecular fragments in RxnIP?
A: At molecular fragments, users can get molecular fragments for a molecule.
Q: How to get reaction difference fingerprints in RxnIP?
A: At reaction difference fingerprints, users can obtain reaction difference fingerprints for a reaction.
Q: Where to calculate reaction distance of two reactions?
A: At reaction distance, users can calculate reaction distance for two reactions.
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