The trRosetta server for fast and accurate protein structure prediction
The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …
14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon
Large-language models (LLMs) such as GPT-4 caught the interest of many scientists.
Recent studies suggested that these models could be useful in chemistry and materials …
Recent studies suggested that these models could be useful in chemistry and materials …
[HTML][HTML] DeePMD-kit v2: A software package for deep potential models
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics
simulations using machine learning potentials known as Deep Potential (DP) models. This …
simulations using machine learning potentials known as Deep Potential (DP) models. This …
ColabFold: making protein folding accessible to all
ColabFold offers accelerated prediction of protein structures and complexes by combining
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
PROTAC-DB 2.0: an updated database of PROTACs
Proteolysis targeting chimeras (PROTACs), which harness the ubiquitin-proteasome system
to selectively induce targeted protein degradation, represent an emerging therapeutic …
to selectively induce targeted protein degradation, represent an emerging therapeutic …
CASTp 3.0: computed atlas of surface topography of proteins
Geometric and topological properties of protein structures, including surface pockets, interior
cavities and cross channels, are of fundamental importance for proteins to carry out their …
cavities and cross channels, are of fundamental importance for proteins to carry out their …
Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model
We report two generative deep-learning models that predict amino acid sequences and 3D
protein structures on the basis of secondary-structure design objectives via either the overall …
protein structures on the basis of secondary-structure design objectives via either the overall …
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
Protein–protein interactions (PPIs) play an important role in the different functions of cells,
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …
GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins
M Chen, W Zhang, Y Gou, D Xu, Y Wei… - Nucleic acids …, 2023 - academic.oup.com
Protein phosphorylation, catalyzed by protein kinases (PKs), is one of the most important
post-translational modifications (PTMs), and involved in regulating almost all of biological …
post-translational modifications (PTMs), and involved in regulating almost all of biological …
Improvements to the APBS biomolecular solvation software suite
Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages that have …
the equations of continuum electrostatics for large biomolecular assemblages that have …