Nucleo is an open-source library for building the nucleotide chains. You give to Nucleo the library of molecules (building blocks), each with one or two R-sites. Then you specify the sequence of block names. Nucleo builds the whole nucleotide chain. You can then get the following characteristics of the chain:

• Canonical SMILES (see Cano for details)
• Molecular mass
• Gross formula

Similarly, you can obtain any of these characteristics for each specific nucleotide.

Input molecules are given in MDL (Symyx) Molfile format.

Nucleo is written in portable C++ and supports the 32-bit and 64-bit versions of the Linux and Microsoft Windows operating systems. No third-party components are used.

Nucleo exposes the C interface to applications. JNI wrapper can be deployed for using Nucleo in Java applications. See JNI Reference for details.

All operation of Nucleo is thread-safe, and so there is no problem to use it in multi-threaded applications.

The nucleotides are:

The canonical SMILES of the nucleotides are:

x00: [&1]
x01: [&1]C
a00: [&1]OC[C@@H]1O[C@H]([C@H](O)[C@@H](-1)O[&2])[nH0]1c[nH0]c2c(:1)[nH0]c[nH0]c(:2)N
c00: [&1]OC[C@@H]1O[C@H]([C@H](O)[C@@H](-1)O[&2])N1C=CC(N)=NC(-1)=O
g00: [&1]OC[C@@H]1O[C@H]([C@H](O)[C@@H](-1)O[&2])[nH0]1c[nH0]c2c(:1)N=C(N)NC(-2)=O
u00: [&1]OC[C@@H]1O[C@H]([C@H](O)[C@@H](-1)O[&2])N1C=CC(=O)NC(-1)=O
p00: [&1]P([&2])([O-])=O
p01: [&1]P([&2])(=O)[S-]

The chain is: x00 p00 a00 p01 u00 p01 g00 p00 c00 x01.

The canonical SMILES of the chain is:

CO[C@@H]1[C@H](COP([O-])(=O)O[C@@H]2[C@H](COP(=O)([S-])O[C@@H]3[C@H](COP(=O)([S-])O[C@@H]4[C@H](COP([O-])=O)O[C@@H]([C@H](-4)O)[nH0]4c[nH0]c5c(:4)[nH0]c[nH0]c(:5)N)O[C@@H]([C@H](-3)O)N3C=CC(=O)NC(-3)=O)O[C@@H]([C@H](-2)O)[nH0]2c[nH0]c3c(:2)N=C(N)NC(-3)=O)O[C@@H]([C@H](-1)O)N1C=CC(N)=NC(-1)=O

The molecular weight of the chain is: 1329.900513.

The gross formula of the chain is: C39 H47 N15 O26 P4 S2.

Look at the Downloads page for the installation package suitable for your system.

See also JNI Reference.

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