A mixed-integer optimization framework for de novo peptide identification
نویسندگان
چکیده
منابع مشابه
A Mixed-Integer Optimization Framework for De Novo Peptide Identification.
A novel methodology for the de novo identification of peptides by mixed-integer optimization and tandem mass spectrometry is presented in this article. The various features of the mathematical model are presented and examples are used to illustrate the key concepts of the proposed approach. Several problems are examined to illustrate the proposed method's ability to address (1) residue-dependen...
متن کاملDe Novo Peptide Identification Via Mixed-Integer Linear Optimization And Tandem Mass Spectrometry
A novel methodology for the de novo identification of peptides via mixedinteger linear optimization (MILP) and tandem mass spectrometry is presented. The overall mathematical model is presented and the key concepts of the proposed approach are described. A pre-processing algorithm is utilized to identify important m/z values in the tandem mass spectrum. Missing peaks, due to residue-dependent f...
متن کاملDe Novo Protein Design" An Interplay of Global Optimization, Mixed-Integer Optimization and Experiments
A major challenge in computational peptide and protein design is the systematic generation of novel peptides and proteins which are either compatible with existing target template structures or with arbitrarily postulated new three dimensional structural folds. In this paper, an account of the recent advances in de novo protein design is presented, followed by background and previous work on th...
متن کاملMISO: Mixed-Integer Surrogate Optimization Framework
We introduce MISO, the Mixed-Integer Surrogate Optimization framework. MISO aims at solving computationally expensive black-box optimization problems with mixed-integer variables. Although encountered in many applications, such as optimal reliability design or structural optimization, for example, where time consuming simulation codes have to be run in order to obtain an objective function valu...
متن کاملMixed-Integer Nonlinear Optimization
Many optimal decision problems in scientific, engineering, and public sector applications involve both discrete decisions and nonlinear system dynamics that affect the quality of the final design or plan. These decision problems lead to mixed-integer nonlinear programming (MINLP) problems that combine the combinatorial difficulty of optimizing over discrete variable sets with the challenges of ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: AIChE Journal
سال: 2006
ISSN: 0001-1541,1547-5905
DOI: 10.1002/aic.11061