B. Erman

How many bits of information can be transferred between residues in a protein and how fast?

The paper quantifies information transfer between protein residues using theoretical models and experimental data, finding transfer rates up to megabits per second.

Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein

This study uses molecular dynamics simulations to analyze how three nanobodies bind to SARS-CoV-2 Spike RBD and affect ACE2 binding, revealing differences in their neutralizing mechanisms against variants.

Synchronous and Asynchronous Response in Dynamically Perturbed Proteins

This study develops a Dynamic Gaussian Network Model to analyze protein perturbation and response, revealing synchronous and asynchronous dynamics and their role in allostery.

Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras

This study compares the local conformational changes and dynamics of four K-Ras oncogenic mutants using molecular dynamics simulations to inform inhibitor development.

Fluctuation, correlation and perturbation-response behavior of nature-made and artificial nanobodies

The paper analyzes how mutations in nanobody CDRs affect protein dynamics using a computational model, identifying residues with different perturbation responses.

ModiBodies: A computational method for modifying nanobodies to improve their antigen binding affinity and specificity

This paper introduces ModiBodies, an algorithm that modifies nanobodies to enhance their antigen binding affinity and specificity through computational mutation of CDR domains.

How many bits of information can be transferred within a protein and how fast?

The paper quantifies information transfer between protein residues using transfer entropy, showing significant long-range information transfer and high transfer rates in PSD-95.

Oncogenic G12D mutation alters local conformations and dynamics of K-Ras

This study uses molecular dynamics simulations to show that the G12D mutation in K-Ras alters local conformations and dynamics, particularly in Switch-II and 3-helix regions, leading to a catalytically impaired state.

Causality, Transfer Entropy and Allosteric Communication Landscapes inProteins with Harmonic Interactions

The paper introduces a method to generate allosteric communication landscapes in proteins using entropy transfer and Gaussian Network Models, showing information transfer occurs through multiple pathways and causality is essential for accurate predictions.