Energy-driven innovations in computational de novo protein engineering

2026/01/21 by Kevser Kübra Kırboğa, Ecir Uğur Küçüksille · 1 voice
Biochemistry, Genetics and Molecular Biology · #Biochemical and Structural Characterization #Protein Structure and Dynamics #RNA and protein synthesis mechanisms

paper · doi:10.1016/j.pbiomolbio.2026.01.005

openalex publication_date 2026/01/21 · crossref created 2026/01/21 · openalex created_date 2026/01/22 · crossref issued 2026/03/01 · crossref published 2026/03/01 · crossref published-print 2026/03/01 · crossref deposited 2026/03/20 · crossref indexed 2026/06/25 · openalex updated_date 2026/07/23

Citations

• Hydrogen bonding in globular proteins
• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
• Protein folding: Defining a “standard” set of experimental conditions and a preliminary kinetic data set of two‐state proteins
• Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
• Scalable molecular dynamics on CPU and GPU architectures with NAMD
• De novo design of protein structure and function with RFdiffusion
• The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach
• Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations
• Conformational ensembles reveal the origins of serine protease catalysis
• Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies
• How the ribosome shapes cotranslational protein folding

Discussions

• Paper: https://doi.org/10.1016/j.pbiomolbio.2026.01.005 Newsletter: https://recep2244.github.io/portfolio/newsletter/2026-01-26-issue-32/ [bsky, 0 points, 0 comments]