Journal of chemical theory and computation
32427471
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Protein molecules are inherently dynamic and modulate their interactions with different molecular partners by accessing different tertiary structures under physiological conditions. Elucidating such structures remains challenging. Current momentum in...
Protein 3D structure prediction has advanced significantly in recent years due to improving contact prediction accuracy. This improvement has been largely due to deep learning approaches that predict inter-residue contacts and, more recently, distanc...
The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting pro...
Residue co-evolution has become the primary principle for estimating inter-residue distances of a protein, which are crucially important for predicting protein structure. Most existing approaches adopt an indirect strategy, i.e., inferring residue co...
Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we p...
Substantial progresses in protein structure prediction have been made by utilizing deep-learning and residue-residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by inc...
As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted featu...