Computational protocol: Structural Characterisation of Ligand-Binding Determinants in Human Lung Surfactant Protein D: Influence of Asp325

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Protocol publication

[…] Isomorphism was sufficient to allow the coordinates of the previously determined 1.6-Å rfhSP-D structure to be used as a starting model for the ligand-bound rfhSP-D structures. The structures were refined using the programs X-PLOR (initially) and CNS. Maps were calculated using CNS and the CCP4 program suite, including density modification (solvent flattening and histogram matching, but not NCS averaging), and models were built using the graphics program O. Topology and parameter files for ligand were obtained from the HIC-Up server. Refinement statistics are given in . All main- and side-chain stereochemical parameters either fall inside or are better than those expected (PROCHECK) with no residues in generously allowed or disallowed regions. Molecular figures were generated using MOLSCRIPT. […]

Pipeline specifications

Software tools CNS, CCP4, PROCHECK, MolScript
Databases HIC-Up
Applications Drug design, Protein structure analysis
Organisms Homo sapiens
Chemicals Disaccharides