Fragment-Based Restricted Active Space Configuration Interaction with Second-order corrections Embedded in Periodic Hartree-Fock Wavefunction

We present a computational scheme for restricted-active-space configuration inter- action (RASCI) calculations combined with second-order perturbation theory (RASCI- PT2) on a fragment of a periodic system embedded in the periodic Hartree-Fock (HF) wavefunction. This method allows one to calculate the electronic structure of localized strongly-correlated features in crystals and surfaces. The scheme was implemented via an interface between the Cryscor and Q-Chem codes. To evaluate the performance of the embedding method, we explored dissociation of fluorine atom from a lithium flu- oride surface and partially fluorinated graphane layer. The results show that RASCI and RASCI-PT2 embedded in periodic HF are able to produce well-behaved potential energy surfaces and accurate dissociation energies.</div

Additional file 5 of Evaluating tools for transcription factor binding site prediction

Evaluation of search tools using PWMs generated from the ENCODE-ChIP-Seq data using rGADEM. Sensitivity, Positive predictive value, Geometric accuracy and False positive rate for the 12 TFBSs that are found in the PAZAR-E dataset. Separate sheets are provided for each of the search tools. (XLS 29.5 kb

Additional file 1 of Evaluating tools for transcription factor binding site prediction

The PAZAR Reference Dataset. Entries from PAZAR, with the numbers of each TFBS that they contain. The spreadsheet also indicates whether the TFBSs are found in JASPAR and/or the ENCODE-ChIP-Seq data. (XLS 54 kb

Additional file 4 of Evaluating tools for transcription factor binding site prediction

Sequence Logos. Sequence logos for the first PWM generated for the 12 TFBSs using each of the four motif discovery tools. (PDF 29.5 kb

Additional file 2 of Evaluating tools for transcription factor binding site prediction

Evaluation of search tools using JASPAR.2010 PWMs. Sensitivity, Positive predictive value, Geometric accuracy and False positive rate for the 14 TFBSs that are found in the PAZAR-J dataset. Separate sheets are provided for each of the search tools. (XLS 31.5 kb