AUTOMUTE PROTEIN MANUAL
AUTOMUTE PROTEIN SOFTWARE

wedger processes a single wedge of data by using mosflm ( 6). Four programs make up the first level of elves automation. Green wedges indicate the scope of each elves program.

AUTOMUTE PROTEIN SOFTWARE

elves automates widely used crystallographic software ( Lower) that are currently run by means of user-specified scripts. As an expert system, elves chooses reasonable starting input parameters for each step, optimizes parameters, and marshals several strategies to detect and overcome common failures in the calculations.įig. 1) were used to carry out individual steps or groups of steps under user direction. In most of these cases, the elves programs wedger, scaler, phaser, and refmacer ( Fig. These structures, solved in several different laboratories, include the human TRAF2/CD40 complex ( 14), the human papilloma virus E2 protein ( 15), aspartate transcarbamoylase ( 16), Escherichia coli primase ( 17), the tandem bromo domains of human TAF250 ( 18), the dimerization domain of hepatocyte nuclear factor 1α ( 19), the human MIA protein ( 20), the replication initiation factor, DnaA ( 21), a designed ankyrin repeat motif ( 22), and the PknB Ser/Thr protein kinase ( 23). elves programs have been used to speed and optimize steps in the determination of many x-ray crystal structures ranging from 8 to 330 kDa in the crystallographic asymmetric unit (au).

AUTOMUTE PROTEIN MANUAL

We developed the expert system elves to automate analysis of crystallographic data without precluding manual control of the process ( Fig. These methods to speed individual computational steps have created the opportunity to fully automate macromolecular x-ray structure determination. Comprehensive program packages such as the CCP4 suite ( 5) have integrated diverse methods through standardized interfaces and file structures. The arp/ warp program enabled automated model building and refinement ( 4). In particular, the solve and resolve programs have been adopted widely for locating heavy atoms, calculating electron density maps, and modeling ( 2, 3). X-ray structural analysis has been facilitated recently by new experimental methods such as multiwavelength anomalous diffraction (MAD) analysis ( 1) and by powerful new algorithms for locating heavy atoms, model building, and structural refinement.

Any step can fail, and the manifold computational inputs generally prevent optimization of any step. Implementation of the random forest algorithm, for classifying mutant activity as either unaffected or affected relative to the native protein, yields 84% accuracy based on tenfold cross-validation.Determining the crystal structure of a large molecule is generally a complicated, multistep process that requires considerable time and training to accomplish. The proteins are diverse with respect to host organism (viral, bacterial, human) and function (enzymatic, nucleic acid binding, signaling), the structures span all four major SCOP classifications, and the mutations occur at positions well distributed throughout the seven structures.

A computational mutagenesis methodology founded upon a structure-dependent and knowledge-based four-body statistical potential is utilized in generating feature vectors that characterize over 8500 individual amino acid substitutions occurring in seven proteins, each mutant having been experimentally ascertained for its relative effect on native protein activity.

Automute protein