25 papers · ranked by Valyu relevance
Aleix Gimeno, María José Ojeda-Montes, Sarah Tomás-Hernández, Adrià Cereto-Massagué + 4 more
'Adrià Cereto-Massagué' 'Raúl Beltrán-Debón' 'Miquel Mulero' 'Gerard Pujadas' 'Santiago Garcia-Vallvé'] Virtual screening consists of using computational tools to predict potentially bioactive compounds from files containing large libraries of small molecules. Virtual screening is becoming increasingly popular in the…
Kauê Santana, Lidiane Diniz do Nascimento, Anderson Lima e Lima, Vinícius Damasceno + 3 more
Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to…
Sebastian Raschka, Anne M. Scott, Nan Liu, Santosh Gunturu + 3 more
While the advantage of screening vast databases of molecules to cover greater molecular diversity is often mentioned, in reality, only a few studies have been published demonstrating inhibitor discovery by screening more than a million compounds for features that mimic a known three-dimensional ligand. Two factors…
Beatriz Suay-García, Jose I. Bueso-Bordils, Antonio Falcó, Gerardo M. Antón-Fos + 3 more
'Gerardo M. Antón-Fos' 'Pedro A. Alemán-López' 'Gary A. Piazza' 'Jia-Zhong Li'] Traditionally, drug development involved the individual synthesis and biological evaluation of hundreds to thousands of compounds with the intention of highlighting their biological activity, selectivity, and bioavailability, as well as…
Grigorii V. Andrianov, Emeline Haroldsen, John Karanicolas
Enthusiastic adoption of make-on-demand chemical libraries for virtual screening has highlighted the need for methods that deliver improved hit-finding discovery rates. Traditional virtual screening methods are often inaccurate, with most compounds nominated in a virtual screen not engaging the intended target protein…
Tristan Bereau
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum methods. The physics-based approach makes MD appropriate to study emergent phenomena…
Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali + 3 more
Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a…
Davide Bassani, Stefano Moro, Marco Tutone, Anna Maria Almerico
The application of computational approaches in drug discovery has been consolidated in the last decades. These families of techniques are usually grouped under the common name of “computer-aided drug design” (CADD), and they now constitute one of the pillars in the pharmaceutical discovery pipelines in many academic…
N. Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali + 2 more
'Gianluca Palermo' 'Stefano Markidis'] Drug discovery is the most expensive, time demanding and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high affinity binding and specificity…
Josip Mesarić
—Drug development is an expensive and timeconsuming process where thousands of chemical compounds are being tested in order to find those possessing drug-like properties while being safe and effective. One of key parts of the early drug discovery process has become virtual drug screening - a method used to narrow down…
Yusuf Adeshina, Eric Deeds, John Karanicolas
With the recent explosion in the size of libraries available for screening, virtual screening is positioned to assume a more prominent role in early drug discovery’s search for active chemical matter. Modern virtual screening methods are still, however, plagued with high false positive rates: typically, only about 12%…
Authors not listed
The imperative to screen ultra-large chemical libraries necessitates high-throughput computational tools capable of efficiently leveraging all available structural and chemical information. We introduce UniDock-Pro, a unified platform built upon the GPU-accelerated Uni-Dock architecture, which integrates…
Toni Sivula, Laxman Yetukuri, Tuomo Kalliokoski, Heikki Käsnänen + 2 more
The emergence of ultra-large screening libraries, filled to the brim with billions of readily available compounds, poses a growing challenge for docking-based virtual screening. Machine Learning (ML) boosted strategies like the tool HASTEN combine rapid ML prediction with the brute-force docking of small fractions of…
Hezha O. Rasul, Dlzar D. Ghafour, Bakhtyar K. Aziz, Bryar A. Hassan + 2 more
'Tarik A. Rashid' 'Arif Kıvrak'] The drug development process is a critical challenge in the pharmaceutical industry due to its timeconsuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable…
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…
Hyun-Myung Woo, Xiaoning Qian, Tan Li, Shantenu Jha + 3 more
'Francis J. Alexander' 'Edward R. Dougherty' 'Byung-Jun Yoon'] The need for efficient computational screening of molecular candidates that possess desired properties frequently arises in various scientific and engineering problems, including drug discovery and materials design. However, the large size of the search…
Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj
Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While math-ematical modeling and machine learning have become vital in predicting drug-target interactions and properties, there is untapped potential in computational drug discovery due to the vast and complex…
Moayad Alnammi, Shengchao Liu, Spencer S Ericksen, Gene E Ananiev + 6 more
Traditional small molecule drug discovery is a time consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine learning methods for virtual chemical screening enables training models on known active and…
Austin Clyde, Ashka Shah, Max Zvyagin, Arvind Ramanathan + 1 more
'Rick Stevens'] Scaffold based drug discovery (SBDD) is a technique for drug discovery which pins chemical scaffolds as the framework of design. Scaffolds, or molecular frameworks, organize the design of compounds into local neighborhoods. We formalize scaffold based drug discovery into a network design. Utilizing…
Moayad Alnammi, Shengchao Liu, Spencer S Ericksen, Gene E Ananiev + 6 more
Traditional small molecule drug discovery is a time consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine learning methods for virtual chemical screening enables training models on known active and…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Jürgen Bajorath
Computational approaches are an integral part of interdisciplinary drug discovery research. Understanding the science behind computational tools, their opportunities, and limitations is essential to make a true impact on drug discovery at different levels. If applied in a scientifically meaningful way, computational…
Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev + 7 more
Prediction of compounds that are active against a desired biological target is a common step in drug discovery efforts. Virtual screening methods seek some active-enriched fraction of a library for experimental testing. Where data are too scarce to train supervised learning models for compound prioritization, initial…
Lili X. Peng, Morgan Lawrenz, Diwakar Shukla, Grace W. Tang + 2 more
Recent molecular dynamics (MD) simulations of the catalytic domain of the c-Src kinase revealed intermediate conformations with a potentially druggable allosteric pocket adjacent to the C-helix, bound by 8-anilino-1-naphthalene sulfonate. Towards confirming the existence of this pocket, we have developed a novel lead…
akhil kumar
Motivation: Screening large libraries virtually can be impractical and computationally expensive, especially when designing dual inhibitors. This is because each target must be screened separately, which further increases the time and resources required. One solution to this problem is to explore the biologically…