Related papers: Improved fragment-based movement with LRFragLib fo…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
In this work, we introduce AutoFragDiff, a fragment-based autoregressive diffusion model for generating 3D molecular structures conditioned on target protein structures. We employ geometric vector perceptrons to predict atom types and…
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
The complex dynamics of agile robotic legged locomotion requires motion planning to intelligently adjust footstep locations. Often, bipedal footstep and motion planning use mathematically simple models such as the linear inverted pendulum,…
Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…
Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…
Surface electromyographic (sEMG) signal serve as a signal source commonly used for lower limb movement recognition, reflecting the intent of human movement. However, it has been a challenge to improve the movements recognition rate while…
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries…
This paper proposes an approach for segmenting a task consisting of compliant motions into phases, learning a primitive for each segmented phase of the task, and reproducing the task by sequencing primitives online based on the learned…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Meshless methods are often used in numerical simulations of systems of partial differential equations (PDEs), particularly those which involve complex geometries or free surfaces. Here we present a novel compact scheme based on the local…
Walking is a key movement of interest in biomechanics, yet gold-standard data collection methods are time- and cost-expensive. This paper presents a real-time, multimodal, high sample rate lower-limb motion capture framework, based on…
While the animals' Fin-to-Limb evolution has been well-researched in biology, such morphological transformation remains under-adopted in the modern design of advanced robotic limbs. This paper investigates a novel class of overconstrained…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…