Related papers: Reconstruction of protein structures from a vector…
Computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show exceptional…
This paper presents a simple yet powerful method for 3D human mesh reconstruction from a single RGB image. Most recently, the non-local interactions of the whole mesh vertices have been effectively estimated in the transformer while the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Microstructure reconstruction is an important cornerstone to the inverse materials design concept. In this work, a general algorithm is developed to reconstruct a three-dimensional microstructure from given descriptors. Based on…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Protein representation learning methods have shown great potential to yield useful representation for many downstream tasks, especially on protein classification. Moreover, a few recent studies have shown great promise in addressing…
The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of…
We introduce a novel framework for learning vector representations of tree-structured geometric data focusing on 3D vascular networks. Our approach employs two sequentially trained Transformer-based autoencoders. In the first stage, the…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose…
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…
The equivalent nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures?…
We investigate combinatorial properties of certain configurations of a graph partition which are related to the minimality of a cut. We show that such configurations are related to the third eigenvector of the Laplacian matrix. It is well…
We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
In this work we show how to construct connectivity kernels induced by the receptive profiles of simple cells of the primary visual cortex (V1). These kernels are directly defined by the shape of such profiles: this provides a metric model…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
3D Morphable Model (3DMM) based methods have achieved great success in recovering 3D face shapes from single-view images. However, the facial textures recovered by such methods lack the fidelity as exhibited in the input images. Recent work…
An amino acid sequence of a protein may be decomposed into consecutive overlapping strings of length K. How unique is the converse, i.e., reconstruction of amino acid sequences using the set of K-strings obtained in the decomposition? This…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…