HOPE: A Homotopy Optimization Method for Protein Structure Prediction

Dunlavy, Daniel M.; O’Leary, Dianne P.; Klimov, Dmitri K.; Thirumalai, D.

doi:10.1089/cmb.2005.12.1275

Cited by 33 publications

(29 citation statements)

References 25 publications

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“…Provided we are always finding the minimum of H(p, λ) with an initial guess that is close to its global minimum, it is more likely that we will find the global minimum of the function F (p). A variant of this method has been successfully applied to complex optimization problems involving protein structures [6] and to finding the equilibrium configuration of an elastica [28]. Note that the choice of known function G(p) is nontrivial.…”

Section: Problem Statementmentioning

confidence: 99%

Parameter identification in dynamic systems using the homotopy optimization approach

et al. 2011

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Identifying the parameters in a mathematical model governed by a system of ordinary differential equations is considered in this work. It is assumed that only partial state measurement is available from experiments, and that the parameters appear nonlinearly in the system equations. The problem of parameter identification is often posed as an optimization problem, and when deterministic methods are used for optimization, one often converges to a local minimum rather than the global minimum. To mitigate the problem of converging to local minima, a new approach is proposed for applying the homotopy technique to the problem of parameter identification. Several examples are used to demonstrate the effectiveness of the homotopy method for obtaining global minima, thereby successfully identifying the system parameters.

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Section: Problem Statementmentioning

confidence: 99%

Parameter identification in dynamic systems using the homotopy optimization approach

et al. 2011

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“…As we are always finding the minimum of H(x, λ) with an initial guess that is close to its global minimum, it is more likely that we will find the global minimum of the function F(x) (if we choose small enough ∆ parameter). A variant of this method has been successfully applied to complex optimization problems involving protein structures [36] and to find the equilibrium configuration of an elastica [37]. Note that the choice of known function G(x) is nontrivial.…”

Section: A Homotopy Optimization Methodsmentioning

confidence: 99%

Directional enlargement of attraction domain via HOPE method

Khajehpour

Moghaddam

2013

2013 21st Iranian Conference on Electrical Engineering (ICEE)

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Extending the domain of attraction is an intresting topic in nonlinear system's survey. In this paper we focus on extending DA along a spesific direction which is denoted by fault running vector. Directional extension is presented by a nonlinear conditioanal optimization problem. As the proposed cost function includes the initial state, a proper choice of starting point which converges to global minimum is difficult. To overcome this problem we use Homotopy Optimization method(HOM). In this method the algorithm starts from minimizing a simple function with a well defined global minimum and during the next iterations the starting cost function is converges to the actual one by uniform variations of homotopy coefficiant. To avoid local minimums we use a combinational algorithm which contains SA and HOM in Homotopy Optimization with Perturbation and Ensembles (HOPE). The simulation results show the eficiency of HOPE method in solving optimization problem of directional enlargement of DA. Moreover, using this idea we effectively increase the critical clearing time of power systems.

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“…There are many different approaches for 3D structure predictions, varying from homology-based to first-principlebased approaches [81][82][83][84][85][86][87]. While all these methods have strengths and weaknesses, from point of view of delivering high quality 3D models, including models for large proteins, the homology-based approaches are far superior to the rest.…”

Section: Progress Made In Structural Genomic Consortiums and 3d Strucmentioning

confidence: 99%

Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine

Alexov

2014

Advances in Biology

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Advances in several biology-oriented initiatives such as genome sequencing and structural genomics, along with the progress made through traditional biological and biochemical research, have opened up a unique opportunity to better understand the molecular effects of human diseases. Human DNA can vary significantly from person to person and determines an individual’s physical characteristics and their susceptibility to diseases. Armed with an individual’s DNA sequence, researchers and physicians can check for defects known to be associated with certain diseases by utilizing various databases. However, for unclassified DNA mutations or in order to reveal molecular mechanism behind the effects, the mutations have to be mapped onto the corresponding networks and macromolecular structures and then analyzed to reveal their effect on the wild type properties of biological processes involved. Predicting the effect of DNA mutations on individual’s health is typically referred to as personalized or companion diagnostics. Furthermore, once the molecular mechanism of the mutations is revealed, the patient should be given drugs which are the most appropriate for the individual genome, referred to as pharmacogenomics. Altogether, the shift in focus in medicine towards more genomic-oriented practices is the foundation of personalized medicine. The progress made in these rapidly developing fields is outlined.

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HOPE: A Homotopy Optimization Method for Protein Structure Prediction

Cited by 33 publications

References 25 publications

Parameter identification in dynamic systems using the homotopy optimization approach

Parameter identification in dynamic systems using the homotopy optimization approach

Directional enlargement of attraction domain via HOPE method

Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine

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