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In our model for RNA secondary structure formation we assume that each of the candidate helices (see definition in the main text) may exist in two states. A helix can be completely zipped, or it can be completely decayed. ... The following schema is used to estimate the effective transition constants between zipped and decayed states: . ... To determine the kinetic constants, we use the transition state theory, which is often used in chemical kinetics (Figure 2). ... Transition . ...

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A program for alignment of structures of DNA-protein complexes . ... Help . ... StructAlign is a program for alignment of DNA-protein complexes' structures. The program gets a pair of complexes of DNA double helix with proteins in PDB-format and optionaly names of protein chains and outputs an alignment of DNA chains corresponding to the best spatial fit of protein chains also in PDB-format. ... X-axis is directed from P atom to C1' atom. ...

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External modules for the Gibbs program The Gibbs program has several built-in non-ideality models which can be used for the calculation of activity coefficients for real solutions: the extended Debye-HЭckel model for aqueous solutions, the modified Peng- Robinson model for gaseous (or liquid) solutions, the Non-Random-Two-Liquid model for liquid solutions, the Mixing-on-Sites model for solid solutions, Subregular and Redlich-Kister models for solid and liquid solutions. ... Attach external modules). ...

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