26 papers · ranked by Valyu relevance
Ilya A. Vakser, Sergei Grudinin, Nathan W. Jenkins, Petras J. Kundrotas + 1 more
Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, so far, have included protein docking and molecular simulation. The latter approaches…
Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Kolinski
Most of the protein-protein docking methods treat proteins as almost rigid objects. Only the side-chains flexibility is usually taken into account. The few approaches enabling docking with a flexible backbone typically work in two steps, in which the search for protein-protein orientations and structure flexibility are…
Shuai Liu, Enyang Zhang, Zhenbang Xu, Jingxu Zhang + 1 more
'Andrey V. Savkin'] Considering the complexity of on-orbit assembly during space missions and the super-large size of space structures, this paper presents the design for a new type of docking interface with an androgynous body that exhibits a number of advantages, including high connection strength and a compact…
Jorge Roel-Touris, Alexandre M.J.J. Bonvin, Brian Jiménez-García
The use of experimental information has been demonstrated to increase the success rate of computational macromolecular docking. Many methods use information to post-filter the simulation output while others drive the simulation based on experimental restraints, which can become problematic for more complex scenarios…
Georgios Iakovou, Stephen D. Laycock, Steven Hayward
Molecular Docking in Virtual Reality Using DockIT Authors: ['Georgios Iakovou' 'Stephen D. Laycock' 'Steven Hayward'] Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to…
M. Zebenaya, Toralf Boge, Daniel Choukroun
A hybrid docking simulator is a hardware-in-the-loop (HIL) simulator that includes a hardware element within a numerical simulation loop. One of the goals of performing a HIL simulation at the European Proximity Operation Simulator (EPOS) is the verification and validation of the docking phase in an on-orbit servicing…
Justin Spiriti, Sundar Raman Subramanian, Rohith Palli, Maria Wu + 1 more
There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at the price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often…
M. Zebenaya, Toralf Boge, Rainer Krenn, Daniel Choukroun
The European Proximity Operation Simulator (EPOS) of the DLR-German Aerospace Center is a robotics-based simulator that aims at validating and verifying a satellite docking phase. The generic concept features a robotics tracking system working in closed loop with a force/torque feedback signal. Inherent delays in the…
Cinthia Aguiar, Ihosvany Camps
Objective: The primary objective of this study is to conduct a comprehensive review of the significance of molecular docking in the field of drug discovery. This includes an examination of the various approaches and methods used in molecular docking, as well as an exploration of the techniques used for interpreting and…
Zuzana Jandova, Attilio Vittorio Vargiu, Alexandre M. J. J. Bonvin
Molecular docking excels at creating a plethora of potential models of protein-protein complexes. To correctly distinguish the favourable, native-like models from the remaining ones remains, however, a challenge. We assessed here if a protocol based on molecular dynamics (MD) simulations would allow to distinguish…
Authors not listed
Docking and molecular dynamics are commonly used methods in drug development for the prediction of interactions between the drug in question and the target protein. When used together, docking studies can provide starting structures for molecular dynamics, which can improve the relatively low accuracy of docking but at…
William Sheffler, Erin C. Yang, Quinton Dowling, Yang Hsia + 11 more
Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice…
Kamila Yunas, Amar Singh, Matthew M. Copeland, Andrii M. Tytarenko + 5 more
Protein behavior inside cells is dominated by the crowded nature of the intracellular environment. Progress in structure determination of proteins and protein complexes, based on advances in Artificial Intelligence, provides an opportunity for structure-based modeling of cellular phenomena. Such modeling at the atomic…
Andreas B. Martinsen, Anastasios M. Lekkas, Sébastien Gros
We propose a method for performing autonomous docking of marine vessels using numerical optimal control. The task is framed as a dynamic positioning problem, with the addition of spatial constraints that ensure collision avoidance. The proposed method is an allencompassing procedure for performing both docking…
Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist + 2 more
In drug discovery, computational methods are a key part of making informed design decisions and prioritising compounds. In particular, optimizing compound affinity is a central concern during the early stages of development. In the last 10 years, alchemical free energy (FE) calculations have transformed our ability to…
Authors not listed
In this work, we benchmark 4 selected open source docking engines for use in the cytochrome P450 protein family. The key enzymes family of phase I metabolism is characterized by a wide variety of accepted substrates due to flexible active site. This work is a benchmark study which aims to evaluate the capabilities of…
Isaac Amela, Pedro Delicado, Antonio Gómez, Sílvia Bonàs + 2 more
'Enrique Querol' 'Juan Cedano'] Background Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein…
Bruno Stegani, Emanuele Scalone, Fran Bacic Toplek, Thomas Lohr + 4 more
The computational study of the binding of a ligand to a target protein provides mechanistic insight into the molecular determinants of this process and can improve the success rate of in silico drug design. All-atom molecular dynamics (MD) simulations can be used to evaluate the binding free energy, typically by…
Samuel C. Gill, David Mobley
Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We…
Mohatashem Reyaz Makhdoomi, Vivek Muralidharan, Kuldeep R. Barad, Juan Sandoval + 2 more
'Juan Sandoval' 'Miguel A. Olivares-Méndez' 'Carol Martínez'] Abstract—The paper presents a novel Hardware-In-the-Loop (HIL) emulation framework of on-orbit interactions using onground robotic manipulators. It combines Virtual Forward Dynamic Model (VFDM) for Cartesian motion control of robotic manipulators with an…
Junfeng Gu, Xu Yang, Ling Kang, Jinying Wu + 1 more
Background As a main method of structure-based virtual screening, molecular docking is the most widely used in practice. However, the non-ideal efficacy of scoring functions is thought as the biggest barrier which hinders the improvement of the molecular docking method. Results A new multi-objective strategy for…
Francesco Longo, Alessandro Chiurco, Roberto Musmanno, Letizia Nicoletti
'Letizia Nicoletti'] This article faces the problem of operative and procedural cooperative training in marine ports with particular attention to harbour pilots and port traffic controller. The design and development of an advanced system, equipped with dedicated hardware in the loop, for cooperative training of…
Xiaobin Jiang, Hongxiang Ren, Xin He, Myung-Il Roh
In the development of ship anchorage training systems, the problems of low efficiency and poor fidelity exist in the simulation of flexible anchor chains, and a position-based dynamics (PBD) method is proposed to express the chain movement. To satisfy the requirements of simulating anchoring manipulation, the PBD…
Samuel C. Gill, David Mobley
Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We…
Toby Bell, Simone D'Amico
— This paper presents the design, development, and application of a novel space simulation environment for rapidly prototyping and testing flight software for distributed space systems. The environment combines the flexibility, determin- ism, and observability of software-only simulation with a level of fidelity and…
Severin Sadjina, Lars T. Kyllingstad, Martin Rindarøy, Stian Skjong + 6 more
'Vilmar Æsøy' 'Dariusz Fathi' 'Vahid Hassani' 'Trond Vidar Johnsen' 'Jørgen Bremnes Nielsen' 'Eilif Pedersen'] Here, we present the concept of an open virtual prototyping framework for maritime systems and operations that enables its users to develop re-usable component or subsystem models, and combine them in…