4,287 research outputs found
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
A real-time proximity querying algorithm for haptic-based molecular docking
Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware
Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations
International audienc
Molecular simulations and visualization: introduction and overview
Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building
Immersive Interactive Quantum Mechanics for Teaching and Learning Chemistry
The impossibility of experiencing the molecular world with our senses hampers
teaching and understanding chemistry because very abstract concepts (such as
atoms, chemical bonds, molecular structure, reactivity) are required for this
process. Virtual reality, especially when based on explicit physical modeling
(potentially in real time), offers a solution to this dilemma. Chemistry
teaching can make use of advanced technologies such as virtual-reality
frameworks and haptic devices. We show how an immersive learning setting could
be applied to help students understand the core concepts of typical chemical
reactions by offering a much more intuitive approach than traditional learning
settings. Our setting relies on an interactive exploration and manipulation of
a chemical system; this system is simulated in real-time with quantum chemical
methods, and therefore, behaves in a physically meaningful way.Comment: 16 pages, 4 figure
Interactivity:the missing link between virtual reality technology and drug discovery pipelines
The potential of virtual reality (VR) to contribute to drug design and
development has been recognised for many years. Hardware and software
developments now mean that this potential is beginning to be realised, and VR
methods are being actively used in this sphere. A recent advance is to use VR
not only to visualise and interact with molecular structures, but also to
interact with molecular dynamics simulations of 'on the fly' (interactive
molecular dynamics in VR, IMD-VR), which is useful not only for flexible
docking but also to examine binding processes and conformational changes.
iMD-VR has been shown to be useful for creating complexes of ligands bound to
target proteins, e.g., recently applied to peptide inhibitors of the SARS-CoV-2
main protease. In this review, we use the term 'interactive VR' to refer to
software where interactivity is an inherent part of the user VR experience
e.g., in making structural modifications or interacting with a physically
rigorous molecular dynamics (MD) simulation, as opposed to simply using VR
controllers to rotate and translate the molecule for enhanced visualisation.
Here, we describe these methods and their application to problems relevant to
drug discovery, highlighting the possibilities that they offer in this arena.
We suggest that the ease of viewing and manipulating molecular structures and
dynamics, and the ability to modify structures on the fly (e.g., adding or
deleting atoms) makes modern interactive VR a valuable tool to add to the
armoury of drug development methods.Comment: 19 pages, 3 figure
3D-Stereoscopic Immersive Analytics Projects at Monash University and University of Konstanz
Immersive Analytics investigates how novel interaction and display technologies may support analytical reasoning and decision making. The Immersive Analytics initiative of Monash University started early 2014. Over the last few years, a number of projects have been developed or extended in this context to meet the requirements of semi- or full-immersive stereoscopic environments. Different technologies are used for this purpose: CAVE2™ (a 330 degree large-scale visualization environment which can be used for educative and scientific group presentations, analyses and discussions), stereoscopic Powerwalls (miniCAVEs, representing a segment of the CAVE2 and used for development and communication), Fishtanks, and/or HMDs (such as Oculus, VIVE, and mobile HMD approaches). Apart from CAVE2™ all systems are or will be employed on both the Monash University and the University of Konstanz side, especially to investigate collaborative Immersive Analytics. In addition, sensiLab extends most of the previous approaches by involving all senses, 3D visualization is combined with multi-sensory feedback, 3D printing, robotics in a scientific-artistic-creative environment
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