22 papers · ranked by Valyu relevance
Ram Milan Kumar Verma, Shashi Ranjan Kumar, Hemendra Arya
In this letter, we present a strategy for autonomous docking of autonomous vehicles in three-dimensional space. Docking is a safety-critical task and requires expert piloting skills. Vehicles with autonomous docking capabilities are highly desirable in various applications, such as marine vehicle docking, aerial…
Authors not listed
—Our understanding of the oceans remains limited by sparse and infrequent observations, primarily because current methods are constrained by the high cost and logistical effort of underwater monitoring, relying either on sporadic surveys across broad areas or on long-term measurements at fixed locations. To overcome…
Ian Knight, Khanh Tang, John Irwin
Molecular docking is a widely used technique for leveraging protein structure in ligand discovery, but as a method, it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress towards automation, docking still requires expert guidance, hindering its adoption by a…
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…
Manuel Rueda, Ruben Abagyan
During the last decade we witnessed how computational docking methods became a crucial tool in the search for new drug candidates. The ‘central dogma’ of small molecule docking is that compounds that dock correctly into the receptor are more likely to display biological activity than those that do not dock. This…
Jeff Guo, Jon Paul Janet, Matthias R. Bauer, Eva Nittinger + 6 more
Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-made protocols to maximize impact in small molecule drug discovery projects. A major obstacle of generative…
Fábio G. Martins, Hélder A. Santos, Sérgio F. Sousa
Peptide-protein docking is an increasingly important technique in computational biochemistry and drug discovery, allowing researchers to predict interactions between peptides and proteins and guiding the development of peptide-based therapeutics. This review provides a detailed overview of the current landscape of…
Ankur Dhanik, John S McMurray, Lydia E Kavraki
Background Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow. Results In our earlier work, we…
Authors not listed
The rapid advancements in computational methods have revolutionized drug discovery and development. These methods, ranging from molecular modelling to machine learning algorithms, have drastically increased in number and sophistication. However, a comprehensive understanding of these diverse approaches is essential for…
Gedaliah Knizhnik, Mark Yim
— We describe a docking mechanism and strategy to allow modular self-assembly for the Modboat: an inexpensive, underactuated, oscillating, surface-swimming robot powered by a single motor. Because propulsion is achieved through oscillation, orientation can be controlled only in the average; this complicates docking…
Didier Devaurs, Dinler A Antunes, Sarah Hall-Swan, Nicole Mitchell + 3 more
'Mark Moll' 'Gregory Lizée' 'Lydia E Kavraki'] Background Docking large ligands, and especially peptides, to protein receptors is still considered a challenge in computational structural biology. Besides the issue of accurately scoring the binding modes of a protein-ligand complex produced by a molecular docking tool…
Haohan Min, Zhoujian Li, Yu Yang, Jinyu Chen + 1 more
— Automatic docking has long been a significant challenge in the field of mobile robotics. Compared to other automatic docking methods, visual docking methods offer higher precision and lower deployment costs, making them an efficient and promising choice for this task. However, visual docking methods impose strict…
Gabriele Pozzati, Petras Kundrotas, Arne Elofsson
Scoring docking solutions is a difficult task, and many methods have been developed for this purpose. In docking, only a handful of the hundreds of thousands of models generated by docking algorithms are acceptable, causing difficulties when developing scoring functions. Today’s best scoring functions can significantly…
Ian Knight, Khanh Tang, Olivier Mailhot, John Irwin
Molecular docking is a widely used technique for leveraging protein structure in ligand discovery, but as a method, it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress towards automation, docking still requires expert guidance, hindering its adoption by a…
Jianxiang Zhang, Chao Yang, Yang Zhang, Xiao Chen + 10 more
Commercially available make-on-demand libraries now exceed 100 billion compounds, requiring over 50 years to screen on 2,000 CPU cores using conventional docking. We present two complementary approaches to address this challenge. CombiDOCK, a combinatorial docking framework, enables exhaustive screening at the…
Anthony Steed, Sebastian Friston, Vijay Pawar, David Swapp
Grounded haptic devices can provide a variety of forces but have limited working volumes. Wearable haptic devices operate over a large volume but are relatively restricted in the types of stimuli they can generate. We propose the concept of docking haptics, in which different types of haptic devices are dynamically…
Sandeep Singh, Hemant Kumar Srivastava, Gaurav Kishor, Harinder Singh + 2 more
In the past, many benchmarking studies have been performed on protein-protein and protein-ligand docking however there is no study on peptide-ligand docking. In this study, we evaluated the performance of seven widely used docking methods (AutoDock, AutoDock Vina, DOCK 6, PLANTS, rDock, GEMDOCK and GOLD) on a dataset…
Yuanping He, Bowen Wang, Feifei Zhao, Xingfu Hong + 5 more
'Weihao Xu' 'Ming Liao' 'Fujing Tian' 'Vlasis Mavrantzas'] To address the wear life prediction challenge of Guide Cones in passive compliant connectors under dynamic loads within specialized equipment, this study proposes a dynamic wear modeling and life assessment method based on the improved Archard model. Through…
Mateusz Dyla, Nicolás S. González Foutel, Daniel E. Otzen, Magnus Kjaergaard
Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans…
Kara Stark, Olivia Crowe, Lindsay Lewellyn
Intercellular bridges are essential for fertility in many organisms. The developing fruit fly egg has become the premier model system to study intercellular bridges. During oogenesis, the oocyte is connected to supporting nurse cells by relatively large intercellular bridges, or ring canals. Once formed, the ring…
Natalia Ruiz-Lafuente, Alfredo Minguela, Jose M. Moraleda, Manuel Muro + 1 more
'Manuel Muro' 'Antonio Parrado'] Dedicator-of-cytokinesis (DOCK), a family of guanine-nucleotide exchange factors (GEFs), comprises four subfamilies, named from A to D. DOCK-D comprises DOCK9, DOCK10, and DOCK11. The GEF activity involves translocation from the cytoplasm to the plasma membrane (PM), as assessed by the…
Jenna R. Christensen, Agnieszka A. Kendrick, Joey B. Truong, Adriana Aguilar-Maldonado + 3 more
In eukaryotic cells, intracellular components are organized by the microtubule motors cytoplasmic dynein-1 (dynein) and kinesins, which are linked to cargos via adaptor proteins. While ∼40 kinesins transport cargo toward the plus end of microtubules, a single dynein moves cargo in the opposite direction. How dynein…