What method to use for protein–protein docking?
Highlights•The best servers based on “free” docking methods find acceptable models
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
Performance and its limits in rigid body protein-protein docking
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions
of complex conformations and thus revolutionized protein-protein docking. FFT-based …
of complex conformations and thus revolutionized protein-protein docking. FFT-based …
Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies
A Larrea-Sebal, S Jebari-Benslaiman… - Current Atherosclerosis …, 2023 - Springer
Abstract Purpose of Review Familial hypercholesterolemia (FH) is a hereditary condition
characterized by elevated levels of low-density lipoprotein cholesterol (LDL-C), which …
characterized by elevated levels of low-density lipoprotein cholesterol (LDL-C), which …
Efficient flexible backbone protein–protein docking for challenging targets
Motivation Binding-induced conformational changes challenge current computational
docking algorithms by exponentially increasing the conformational space to be explored. To …
docking algorithms by exponentially increasing the conformational space to be explored. To …
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
We present the performance of HADDOCK, our information-driven docking software, in the
second edition of the D3R Grand Challenge. In this blind experiment, participants were …
second edition of the D3R Grand Challenge. In this blind experiment, participants were …
Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent
The current pandemic of Covid-19 caused by SARS-CoV-2 is continued to spread globally
and no potential drug or vaccine against it is available. Spike (S) glycoprotein is the …
and no potential drug or vaccine against it is available. Spike (S) glycoprotein is the …
Unveiling the functional epitopes of cobra venom cytotoxin by immunoinformatics and epitope-omic analyses
Approximate 70% of cobra venom is composed of cytotoxin (CTX), which is responsible for
the dermonecrotic symptoms of cobra envenomation. However, CTX is generally low in …
the dermonecrotic symptoms of cobra envenomation. However, CTX is generally low in …
iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations
Quantitative evaluation of binding affinity changes upon mutations is crucial for protein
engineering and drug design. Machine learning‐based methods are gaining increasing …
engineering and drug design. Machine learning‐based methods are gaining increasing …
iScore: a novel graph kernel-based function for scoring protein–protein docking models
Motivation Protein complexes play critical roles in many aspects of biological functions.
Three-dimensional (3D) structures of protein complexes are critical for gaining insights into …
Three-dimensional (3D) structures of protein complexes are critical for gaining insights into …
Unlocking novel therapies: Cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning
D de Raffele, IM Ilie - Chemical Communications, 2024 - pubs.rsc.org
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address
only their symptoms and do not prevent disease onset. Common therapeutic agents, such as …
only their symptoms and do not prevent disease onset. Common therapeutic agents, such as …