PMC:4103454 / 26304-27359 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4103454","sourcedb":"PMC","sourceid":"4103454","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4103454","text":"Model Building\nThe FAN1 VRR-Nuc domains (human, mouse, and Pseudomonas) have the same predicted secondary structure using PSIPRED (McGuffin et al., 2000) and therefore likely the same topology as standalone domains except for an insertion consisting of two confidently predicted helices. Twenty models of hFAN1 and pFAN1 were initially built based on the combined crystal structures of the archaeal HJR, HJC (PDB code 1GEF; Nishino et al., 2001), and the SdaI restriction endonuclease (PDB code 2IXS; Tamulaitiene et al., 2006) using the “modeler” option (Sali and Blundell, 1993) in QUANTA (Accelrys). The different models were calculated by varying the initial model and optimizing the objective function using conjugate gradients and molecular dynamics with simulated annealing using the CHARMm force field. The models with the lowest objective function were chosen for further refinement. This consisted of introducing the two helices insertion using the manual modeling options in QUANTA, taking care to ensure proper packing of hydrophobic residues.","divisions":[{"label":"Title","span":{"begin":0,"end":14}}],"tracks":[{"project":"2_test","denotations":[{"id":"24981866-10869041-20021759","span":{"begin":148,"end":152},"obj":"10869041"},{"id":"24981866-11286886-20021760","span":{"begin":440,"end":444},"obj":"11286886"},{"id":"24981866-16962970-20021761","span":{"begin":522,"end":526},"obj":"16962970"},{"id":"24981866-8254673-20021762","span":{"begin":575,"end":579},"obj":"8254673"}],"attributes":[{"subj":"24981866-10869041-20021759","pred":"source","obj":"2_test"},{"subj":"24981866-11286886-20021760","pred":"source","obj":"2_test"},{"subj":"24981866-16962970-20021761","pred":"source","obj":"2_test"},{"subj":"24981866-8254673-20021762","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93eca0","default":true}]}]}}