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Total 981 results found since Jan 2013.

Molecules, Vol. 23, Pages 2106: Mechanisms of Protein Search for Targets on DNA: Theoretical Insights
eisky Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-pa...
Source: Molecules - August 22, 2018 Category: Chemistry Authors: Alexey A. Shvets Maria P. Kochugaeva Anatoly B. Kolomeisky Tags: Review Source Type: research

Molecules, Vol. 26, Pages 7149: SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures
Yamada In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glyca...
Source: Molecules - November 25, 2021 Category: Chemistry Authors: Tsuchiya Matsubara Aoki-Kinoshita Yamada Tags: Technical Note Source Type: research

Molecules, Vol. 24, Pages 1150: Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm
tés Structural elements inserted in proteins are essential to define folding/unfolding mechanisms and partner recognition events governing signaling processes in living organisms. Here, we present an original approach to model the folding mechanism of these structural elements. Our approach is based on the exploitation of local, sequence-dependent structural information encoded in a database of three-residue fragments extracted from a large set of high-resolution experimentally determined protein structures. The computation of conformational transitions leading to the formation of the structural elements is formulated...
Source: Molecules - March 21, 2019 Category: Chemistry Authors: Alejandro Esta ña Malik Ghallab Pau Bernad ó Juan Cort és Tags: Article Source Type: research

Molecules, Vol. 24, Pages 2233: Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search
This study demonstrates that the use of highly curated chemical and biological experimental data on one side, and a powerful multi-fingerprint search algorithm on the other, can be of the utmost importance in addressing the fate of newly conceived small molecules, by strongly reducing the attrition of early phases of drug discovery programs.
Source: Molecules - June 13, 2019 Category: Chemistry Authors: Montaruli Alberga Ciriaco Trisciuzzi Tondo Mangiatordi Nicolotti Tags: Article Source Type: research

Molecules, Vol. 26, Pages 5593: Rapid Identification of Potential Drug Candidates from Multi-Million Compounds ’ Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening
Molecules, Vol. 26, Pages 5593: Rapid Identification of Potential Drug Candidates from Multi-Million Compounds’ Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening Molecules doi: 10.3390/molecules26185593 Authors: Katalin Szilágyi Beáta Flachner István Hajdú Mária Szaszkó Krisztina Dobi Zsolt Lőrincz Sándor Cseh György Dormán Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost-effective approach in early drug discovery. If structures of active compounds are available, rapid ...
Source: Molecules - September 15, 2021 Category: Chemistry Authors: Katalin Szil ágyi Be áta Flachner Istv án Hajdú M ária Szaszkó Krisztina Dobi Zsolt L őrincz S ándor Cseh Gy örgy Dormán Tags: Article Source Type: research

Molecules, Vol. 26, Pages 7201: Greedy 3-Point Search (G3PS) & mdash;A Novel Algorithm for Pharmacophore Alignment
Molecules, Vol. 26, Pages 7201: Greedy 3-Point Search (G3PS)—A Novel Algorithm for Pharmacophore Alignment Molecules doi: 10.3390/molecules26237201 Authors: Christian Permann Thomas Seidel Thierry Langer Chemical features of small molecules can be abstracted to 3D pharmacophore models, which are easy to generate, interpret, and adapt by medicinal chemists. Three-dimensional pharmacophores can be used to efficiently match and align molecules according to their chemical feature pattern, which facilitates the virtual screening of even large compound databases. Existing alignment methods, used in computat...
Source: Molecules - November 27, 2021 Category: Chemistry Authors: Christian Permann Thomas Seidel Thierry Langer Tags: Article Source Type: research

Molecules, Vol. 23, Pages 567: Identification and Characterizations of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Scaffold Hopping- and 2D-Molecular Fingerprint-Based Similarity Search
heng Luo Kai Chen SET7, serving as the only histone methyltransferase that monomethylates ‘Lys-4’ of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What′s more, SET7 is involved inthe pathogenesis of alopecia aerate, breast cancer, tumor and cancer progression, atherosclerosis in human carotid plaques, chronic renal diseases, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and ...
Source: Molecules - March 2, 2018 Category: Chemistry Authors: Hong Ding Wen Lu Jun Hu Yu-Chih Liu Chen Zhang Fu Lian Nai Zhang Fan Meng Cheng Luo Kai Chen Tags: Article Source Type: research

Molecules, Vol. 23, Pages 1876: Be Aware of Aggregators in the Search for Potential Human ecto-5 ′-Nucleotidase Inhibitors
Molecules, Vol. 23, Pages 1876: Be Aware of Aggregators in the Search for Potential Human ecto-5′-Nucleotidase Inhibitors Molecules doi: 10.3390/molecules23081876 Authors: Lucas G. Viviani Erika Piccirillo Arquimedes Cheffer Leandro de Rezende Henning Ulrich Ana Maria Carmona-Ribeiro Antonia T.-do Amaral Promiscuous inhibition due to aggregate formation has been recognized as a major concern in drug discovery campaigns. Here, we report some aggregators identified in a virtual screening (VS) protocol to search for inhibitors of human ecto-5′-nucleotidase (ecto-5′-NT/CD73), a...
Source: Molecules - July 27, 2018 Category: Chemistry Authors: Lucas G. Viviani Erika Piccirillo Arquimedes Cheffer Leandro de Rezende Henning Ulrich Ana Maria Carmona-Ribeiro Antonia T.-do Amaral Tags: Article Source Type: research

Molecules, Vol. 24, Pages 897: Insecticidal and Nematicidal Contributions of Mexican Flora in the Search for Safer Biopesticides
lo Plant metabolites have been used for many years to control pests in animals and to protect crops. Here, we reviewed the available literature, looking for the species of Mexican flora for which extracts and metabolites have shown activity against pest insects and parasitic nematodes of agricultural importance, as well as against nematodes that parasitize domestic cattle. From 1996 to 2018, the search for novel and eco-friendly biopesticides has resulted in the identification of 114 species belonging to 36 botanical families of Mexican plants with reported biological effects on 20 insect species and seven nematode spe...
Source: Molecules - March 3, 2019 Category: Chemistry Authors: Beatriz Hern ández-Carlos Marcela Gamboa-Angulo Tags: Review Source Type: research

Molecules, Vol. 25, Pages 2010: High-Throughput Computational Search for Half-Metallic Oxides
o Nardelli Half metals are a peculiar class of ferromagnets that have a metallic density of states at the Fermi level in one spin channel and simultaneous semiconducting or insulating properties in the opposite one. Even though they are very desirable for spintronics applications, identification of robust half-metallic materials is by no means an easy task. Because their unusual electronic structures emerge from subtleties in the hybridization of the orbitals, there is no simple rule which permits to select a priori suitable candidate materials. Here, we have conducted a high-throughput computational search for half-me...
Source: Molecules - April 24, 2020 Category: Chemistry Authors: Laalitha S. I. Liyanage Jagoda S ławińska Priya Gopal Stefano Curtarolo Marco Fornari Marco Buongiorno Nardelli Tags: Article Source Type: research

Molecules, Vol. 26, Pages 4323: Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
uc In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401624 COCONUT compounds. The introduced drug repurposing pipeline consists of compou...
Source: Molecules - July 16, 2021 Category: Chemistry Authors: Ozren Jovi ć Tomislav Šmuc Tags: Article Source Type: research

Molecules, Vol. 26, Pages 4420: Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search
iao RNA molecules participate in many important biological processes, and they need to fold into well-defined secondary and tertiary structures to realize their functions. Like the well-known protein folding problem, there is also an RNA folding problem. The folding problem includes two aspects: structure prediction and folding mechanism. Although the former has been widely studied, the latter is still not well understood. Here we present a deep reinforcement learning algorithms 2dRNA-Fold to study the fastest folding paths of RNA secondary structure. 2dRNA-Fold uses a neural network combined with Monte Carlo tree sear...
Source: Molecules - July 22, 2021 Category: Chemistry Authors: Kangkun Mao Yi Xiao Tags: Article Source Type: research

Molecules, Vol. 27, Pages 65: Dealing with the Ambiguity of Glycan Substructure Search
Lisacek The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large-scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating these data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge...
Source: Molecules - December 23, 2021 Category: Chemistry Authors: Vincenzo Daponte Catherine Hayes Julien Mariethoz Frederique Lisacek Tags: Article Source Type: research

Molecules, Vol. 27, Pages 3280: In Search of Synergistic Insect Repellents: Modeling of Muscarinic GPCR Interactions with Classical and Bitopic Photoactive Ligands
Nowak Insect vector-borne diseases pose serious health problems, so there is a high demand for efficient molecules that could reduce transmission. Using molecular docking and molecular dynamics (MD) simulation, we studied a series of compounds acting on human and insect muscarinic acetylcholine receptors (mAChRs), a novel target of synergistic agents in pest control. We characterized early conformational changes of human M1 and fruit fly type-A mAChR G protein-coupled receptors (GPCRs) in response to DEET, IR3535, and muscarine binding based on the MD analysis of the activation microswitches known to form the signal tr...
Source: Molecules - May 20, 2022 Category: Chemistry Authors: Beata Niklas Bruno Lapied Wieslaw Nowak Tags: Article Source Type: research

Molecules, Vol. 28, Pages 1240: Energy Level Prediction of Organic Semiconductors for Photodetectors and Mining of a Photovoltaic Database to Search for New Building Units
Mustafa Kamal Due to the large versatility in organic semiconductors, selecting a suitable (organic semiconductor) material for photodetectors is a challenging task. Integrating computer science and artificial intelligence with conventional methods in optimization and material synthesis can guide experimental researchers to develop, design, predict and discover high-performance materials for photodetectors. To find high-performance organic semiconductor materials for photodetectors, it is crucial to establish a relationship between photovoltaic properties and chemical structures before performing synthetic procedures i...
Source: Molecules - January 27, 2023 Category: Chemistry Authors: Jehad Saleh Sajjad Haider Muhammad Saeed Akhtar Muhammad Saqib Muqadas Javed Sayed Elshahat Ghulam Mustafa Kamal Tags: Article Source Type: research