Discussion of “ Equi - Energy Sampler ” by Kou , Zhou and Wong
نویسنده
چکیده
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of a protein chain given the sequence of its amino acid building blocks. The complexity of the problem strongly depends on the protein representation and its energy function. The more detailed the model, the more complex its corresponding energy function and the more challenge it sets for sampling algorithms. Kou, Zhou and Wong have introduced a novel sampling method, which could contribute significantly to the field of structural prediction.
منابع مشابه
Discussion of the paper by Kou, Zhou and Wong
We congratulate Samuel Kou, Qing Zhou and Wing Wong (referred subsequently as KZW) for this beautifully written paper, which opens a new direction in Monte Carlo computation. This discussion has two parts. First, we describe a very closely related method, multicanonical sampling (MCS), and report a simulation example that compares the Equi-Energy (EE) sampler with MCS. Over all, we found the tw...
متن کاملDiscussion of “ Equi - Energy Sampler ” by Kou , Zhou and Wong
1. Questions. To simplify the language, we use π(x) to denote a distribution we want to sample from, and q(x) to denote a distribution at a higher temperature (with energy truncation). The distributions π(x) and q(x) can be understood as two consecutive levels in the EE-sampler. Suppose we have obtained a sample from q(x) by running a Markov chain (with a burn-in period), and let us call the sa...
متن کاملConvergence of the Equi-Energy Sampler and Its Application to the Ising Model.
We provide a complete proof of the convergence of a recently developed sampling algorithm called the equi-energy (EE) sampler (Kou, Zhou, and Wong, 2006) in the case that the state space is countable. We show that in a countable state space, each sampling chain in the EE sampler is strongly ergodic a.s. with the desired steady-state distribution. Furthermore, all chains satisfy the individual e...
متن کاملEqui-Energy Sampler with Applications in Statistical Inference and Statistical Mechanics
We introduce a new sampling algorithm, the equi-energy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperature-domain methods, the equi-energy sampler, utilizing the temperature-energy duality, targets the energy directly. The focus on the energy function not only facilitates efficient sampling, but also provides a powerful means for statistical ...
متن کاملA study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling.
We propose an equi-energy (EE) sampling approach to study protein folding in the two-dimensional hydrophobic-hydrophilic (HP) lattice model. This approach enables efficient exploration of the global energy landscape and provides accurate estimates of the density of states, which then allows us to conduct a detailed study of the thermodynamics of HP protein folding, in particular, on the tempera...
متن کامل