An Introduction to Biomolecular Graphics 英文参考文献.docVIP

Education AnIntroductiontoBiomolecularGraphics CameronMura1*,ColinM.McCrimmon1,JasonVertrees2,MichaelR.Sawaya3 1DepartmentofChemistry,UniversityofVirginia,Charlottesville,Virginia,UnitedStatesofAmerica,2Schro¨dingerLLC,NewYork,NewYork,UnitedStatesofAmerica, 3HowardHughesMedicalInstitute,UniversityofCalifornia,LosAngeles,California,UnitedStatesofAmerica Introduction small-molecule [3] or macromolecular visu- alization[4–6]. the inherent complexity (1,000s of atoms in a protein) at the nanometer scale, in ordertoelucidatemolecularstructureand itsrelationshiptobiologicalfunction.Even morespecifically,withinthecontextofthe scientificstorybeingtold,whatisthemain purpose oftheplanned figure? If afigure attempts to serve too many purposes, it may become cluttered and ineffective. In articulatingthepurposeofthefigure,bear in mind the target audience (Box 2) and the minimum level of detail required to conveythescientificmessage.Thesepoints willhelpdrivechoicesastowhatMolVis approachesandsoftwarepackagesarebest suitedtotheproblemathand. The next step—selecting the optimal tools from among the myriad available softwarepackages—isoftenquitedifficult. Multiple tools are often necessary in the workflow leading to a finalized piece of molecular graphics. For instance, electro- static potentials may be computed in a pre-processing stage, followed by actual scene construction and rendering of grid mapsinPyMOLorVMD,andthenpost- processing in a graphics editing applica- tionsuchasAdobePhotoshop(BoxS1in Text S1). A comprehensive review and comparison of MolVis software suites is beyond the scope of this primer; such useful information has been tabulated recently by Bottomley and Helmerhorst in 2009 (see Table 9.2 in [2]), and by O’Donoghueetal.in2010(seeTable1in [6]). Also, the Protein Data Bank (PDB) offers a thorough, annotated compilation of software [7]. Some of the existing software packages are more monolithic than others, but none is so fully featured thateveryconceivableMolVi