12 papers · ranked by Valyu relevance
Alejandro Martínez León, Lucas Andersen, Jochen S. Hub
User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA Authors: Alejandro Martínez León, Lucas Andersen, Jochen S. Hub We present BindFlow, a Python-based software for automated absolute binding free energy (ABFE) calculations at the free energy perturbation…
Dian Chen, Y. Chen, Tong Lin, Sijie Chen + 1 more
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the inherent conformational flexibility of peptides and the limited availability of…
Yanli Wang, Frimpong Boadu, Jianlin Cheng, Lenore Cowen
MPBind was trained with true protein structures as input. To investigate how well it can predict binding sites from predicted protein structures, we randomly selected 20 protein chains for each of the five kinds of binding sites from Test2_data dataset (i.e. 100 protein chains in total) and applied AlphaFold 3 () to…
Mohammad Abdullah Aljasir, Sajjad Ahmad, Roberta Rocca, Alessia Bono + 1 more
Background/Objectives: GuaB, which is known as inosine 5′-phosphate dehydrogenase (IMPDH), is an enzymatic target involved in the de novo guanine biosynthetic pathway of the multidrug-resistant (MDR) Acinetobacter baumannii. GuaB has emerged as a potential therapeutic target to cope with increasing antibiotic…
Ainur Abukaev, Constantin Völter, Mikhail Romodin, Sebastian Schwartzkopff + 6 more
A new Python package, pygid, enables fast batch processing of X-ray scattering data, with a particular focus on grazing-incidence geometries.
Zeyi Zhang, Carlos Mora Perez, Patrick Kwon, Martin Head‐Gordon + 1 more
PARSEC.py is a Python-based real-space Kohn-Sham density functional theory (real-space KS-DFT) framework designed to provide a user- and developer-friendly platform for first-principles electronic-structure simulations. Discretization on real-space grids eliminates basis-set approximations, while enabling systematic…
Dylan Silke, Julie Iskander, Junqi Pan, Andrew P. Thompson + 3 more
Leveraging artificial intelligence and deep learning to generate proteins de novo (a.k.a. ‘synthetic proteins’) has unlocked new frontiers of protein design. Deep learning models trained on protein structures can generate novel protein designs that explore structural landscapes unseen by evolution. This approach…
Tomasz Chady, Zuzanna Karolina Filutowska, Zhiyong Lu
The eccLib library provides a high-performance solution for parsing GTF and FASTA files in Python, thereby significantly enhancing project performance. eccLib was built with the Python/C API in mind, allowing for performance closely matching that of native C parsers, which would not be feasible if implemented directly…
Liu Xuhan, Zhang Baohua, Zhang, Hong + 1 more
Molecular docking is a cornerstone of drug discovery to unveil the mechanism of ligand-receptor interactions. With the recent development of deep learning in the field of artificial intelligence, innovative methods were developed for molecular docking. However, the mainstream docking programs adopt a…
Wajid Arshad Abbasi, Syed Ali Abbas, Maryum Bibi, Saiqa Andleeb + 1 more
The trade-off between predictive accuracy and data availability makes it difficult to predict protein–protein binding affinity accurately. The lack of experimentally resolved protein structures limits the performance of structure-based machine learning models, which generally outperform sequence-based methods. In order…
Azam Shirali, Vitalii Stebliankin, Jimeng Shi, Prem P. Chapagain + 1 more
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking tools rely on their scoring function. Accurate and efficient scoring functions are…
Hanqun Cao, Aastha Pal, Sophia Tang, Yinuo Zhang + 3 more
Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This is especially important for clinically relevant G protein-coupled receptors (GPCRs), where therapeutic efficacy depends on functional…