De Novo algorithms

Davidsou-Fletcher-Powell (DFP) a geometry optimization algorithm De Novo algorithms algorithms that apply artificial intelligence or rational techniques to solving chemical problems density functional theory (DFT) a computational method based on the total electron density... 

Candid [26] combines features from Noah and Aria, such as the use of three-dimensional structure-based filters and ambiguous distance constraints, with the new concepts of network-anchoring and constraint combination that further enable an efficient and reliable search for the correct fold in the initial cycle of de novo NMR structure determinations. A flowchart of the Candid algorithm is given in Fig. 2.3. 

Two fundamental questions have to be asked about de novo design algorithms ... 

A major problem in predicting protein structure is the computational intractability. A short, 100-residue protein will contain at least 100 side-chain-to-side-chain or side-chain-to-solvent interactions. The orientation of each of these interactions will lead to cascading effects throughout the protein. Comparative modeling, threading algorithms, and de novo predictions seek to predict protein structure in reasonable execution times. 

DA Pearlman, MA Murcko (1993) CONCEPTS New dynamic algorithm for de novo drug suggestion, J Comput Chem 14( 10) 1184—1193... 

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