Related papers: Interactive molecular dynamics in virtual reality …
Dynamic volumetric MRI provides valuable information on in vivo motion and biomechanics, with applications spanning cardiac, musculoskeletal, or pulmonary imaging, amongst others. Developing reconstruction methods for time-resolved…
Head Mounted Displays (HMDs) allow users to experience virtual reality with a great level of immersion. However, even simple physical tasks like drinking a beverage can be difficult and awkward while in a virtual reality experience. We…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
We build on the concept of eigenvector continuation to develop an efficient multi-state method for the rigorous and smooth interpolation of a small training set of many-body wavefunctions through chemical space at mean-field cost. The…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
Mixed Reality (MR) and Virtual Reality (VR) simulations are hampered by requirements for hand controllers or attempts to perseverate in use of two-dimensional computer interface paradigms from the 1980s. From our efforts to produce more…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
The ability to achieve and maintain inverted poses is essential for unlocking the full agility of miniature blimp robots (MBRs). However, developing reliable inverted control strategies for MBRs remains challenging due to their complex and…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
We propose a framework based on Quadratic Unconstrained Binary Optimization (QUBO) for generating plausible ligand binding poses within protein pockets, enabling efficient structure-based virtual screening. The method discretizes the…
This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
During VR demos we have performed over last few years, many participants (in the absence of any haptic feedback) have commented on their perceived ability to 'feel' differences between simulated molecular objects. The mechanisms for such…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…