Related papers: A Hybrid Local Search for Simplified Protein Struc…

The model of low-dimensional manifold and sparse representation are two well-known concise models that suggest each data can be described by a few characteristics. Manifold learning is usually investigated for dimension reduction by…

Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…

We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…

Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it…

De novo prediction of protein structures, the prediction of structures from amino-acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we…

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…

Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…

Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…

CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm's…

Autoencoder-based image codecs achieve state-of-the-art compression performance but often incur high computational complexity, particularly at decoding time. This work introduces a low-complexity learned image compression framework based on…

We investigate the extent to which the commonly used standard pairwise contact potential can be used to identify the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all…

We study Crystal Structure Prediction, one of the major problems in computational chemistry. This is essentially a continuous optimization problem, where many different, simple and sophisticated, methods have been proposed and applied. The…

Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…

Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…

In contrast to comparing faces via single exemplars, matching sets of face images increases robustness and discrimination performance. Recent image set matching approaches typically measure similarities between subspaces or manifolds, while…

In this paper a deterministic preprocessing algorithm is presented, whose output can be given as input to most state-of-the-art epipolar geometry estimation algorithms, improving their results considerably. They are now able to succeed on…

Domain adaptive image retrieval includes single-domain retrieval and cross-domain retrieval. Most of the existing image retrieval methods only focus on single-domain retrieval, which assumes that the distributions of retrieval databases and…