Related papers: High-throughput Binding Affinity Calculations at E…
Motivation: Engineering high-affinity binders targeting specific antigenic determinants remains a challenging and often daunting task, requiring extensive experimental screening. Computational methods have the potential to accelerate this…
Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over…
We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little or no modification to many modern molecular simulation…
Adaptive therapy is a dynamic cancer treatment protocol that updates (or "adapts") treatment decisions in anticipation of evolving tumor dynamics. This broad term encompasses many possible dynamic treatment protocols of patient-specific…
Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems…
Variability in the tumorigenic potential among cancer cells within a tumor population is an unresolved fundamental issue in cancer biology. It is important to know whether cancer cells with higher tumorigenic potential, such as cancer stem…
The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Lung cancer is a condition where there is abnormal growth of malignant cells that spread in an uncontrollable fashion in the lungs. Some common treatment strategies are surgery, chemotherapy, and radiation which aren't the best options due…
Subatomic systems are pivotal for understanding fundamental baryonic interactions, as they provide direct access to quark-level degrees of freedom. In particular, introducing a strange quark adds "strangeness" as a new dimension, offering a…
The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens…
Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon…
Model predictive control (MPC) is an optimization-based control strategy with broad industrial adoption. Unfortunately, the required computation time to solve the receding-horizon MPC optimization problem can become prohibitively large for…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Antibody-based therapeutics-including antibody-drug conjugates (ADCs), bispecific antibodies, and novel formats-are reshaping oncology, yet key determinants of efficacy, safety, and manufacturability frequently emerge after conjugation and…
Resistance to therapy remains a significant challenge in cancer treatment, often due to the presence of a stem-like cell population that drives tumor recurrence post-treatment. Moreover, many anticancer therapies induce plasticity,…
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…