abstract：:Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguis...

journal_title：Journal of chemical information and modeling

authors： Guterres H,Im W

更新日期：2020-04-27 00:00:00

abstract：:Three-dimensional protein structures are a key requisite for structure-based drug discovery. For many highly relevant targets, medicinal chemists are confronted with large numbers of target structures in their apo-forms or in complex with a wealth of different ligands. To exploit the full potential of such structure e...

journal_title：Journal of chemical information and modeling

authors： Schmalhorst PS,Bergner A

更新日期：2020-04-27 00:00:00

abstract：:The number of journal articles in the scientific domain has grown to the point where it has become impossible for researchers to capitalize on all findings in their relevant discipline. Information is stored in these articles in a number of ways, including figures that describe important results. In organic chemistry,...

journal_title：Journal of chemical information and modeling

authors： Beard EJ,Cole JM

更新日期：2020-04-27 00:00:00

abstract：:The primary goal of ligand-based virtual screening is to identify active compounds consisting of a core scaffold that is not found in the current active compound pool. Scaffold hopping is the term used for this purpose. In the present study, topological representations of pharmacophore features on chemical graphs were...

journal_title：Journal of chemical information and modeling

authors： Nakano H,Miyao T,Funatsu K

更新日期：2020-04-27 00:00:00

abstract：:The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, requiring multiple iterations of trial and error designs, an ideal scenario for applying computer ...

journal_title：Journal of chemical information and modeling

authors： Perez C,Soler D,Soliva R,Guallar V

更新日期：2020-03-23 00:00:00

abstract：:Modern industrial lubricants are often blended with an assortment of chemical additives to improve the performance of the base stock. Machine learning-based predictive models allow fast and veracious derivation of material properties and facilitate novel and innovative material designs. In this study, we outline the d...

journal_title：Journal of chemical information and modeling

authors： Loh GC,Lee HC,Tee XY,Chow PS,Zheng JW

更新日期：2020-03-23 00:00:00

abstract：:Atomic neural networks (ANNs) constitute a class of machine learning methods for predicting potential energy surfaces and physicochemical properties of molecules and materials. Despite many successes, developing interpretable ANN architectures and implementing existing ones efficiently are still challenging. This call...

journal_title：Journal of chemical information and modeling

authors： Shao Y,Hellström M,Mitev PD,Knijff L,Zhang C

更新日期：2020-03-23 00:00:00

abstract：:Traditional herbal medicine has been an inseparable part of the traditional medical science in many countries throughout history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practices, has gradually expanded to numerous Western countries with positive impacts and acceptance. T...

journal_title：Journal of chemical information and modeling

authors： Nguyen-Vo TH,Nguyen L,Do N,Nguyen TN,Trinh K,Cao H,Le L

更新日期：2020-03-23 00:00:00

abstract：:The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, deriv...

journal_title：Journal of chemical information and modeling

authors： Kříž K,Řezáč J

更新日期：2020-03-23 00:00:00

abstract：:In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the fie...

journal_title：Journal of chemical information and modeling

authors： Kammeraad JA,Goetz J,Walker EA,Tewari A,Zimmerman PM

更新日期：2020-03-23 00:00:00

abstract：:Ergotamine (ERG) and dihydroergotamine (DHE), common migraine drugs, have small structural differences but lead to clinically important distinctions in their pharmacological profiles. For example, DHE is less potent than ERG by about 10-fold at the 5-hydroxytrptamine receptor 1B (5-HT1B). Although the high-resolution ...

journal_title：Journal of chemical information and modeling

authors： Sullivan HJ,Tursi A,Moore K,Campbell A,Floyd C,Wu C

更新日期：2020-03-23 00:00:00

abstract：:Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on ...

journal_title：Journal of chemical information and modeling

authors： Sandoval-Lira J,Mondragón-Solórzano G,Lugo-Fuentes LI,Barroso-Flores J

更新日期：2020-03-23 00:00:00

abstract：:Reversible and irreversible covalent ligands are advanced cysteine protease inhibitors in the drug development pipeline. K777 is an irreversible inhibitor of cruzain, a necessary enzyme for the survival of the Trypanosoma cruzi (T. cruzi) parasite, the causative agent of Chagas disease. Despite their importance, irrev...

journal_title：Journal of chemical information and modeling

authors： Silva JRA,Cianni L,Araujo D,Batista PHJ,de Vita D,Rosini F,Leitão A,Lameira J,Montanari CA

更新日期：2020-03-23 00:00:00

abstract：:Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description...

journal_title：Journal of chemical information and modeling

authors： Barrera MC,Jorge M

更新日期：2020-03-23 00:00:00

abstract：:One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of...

journal_title：Journal of chemical information and modeling

authors： da Costa CHS,Bonatto V,Dos Santos AM,Lameira J,Leitão A,Montanari CA

更新日期：2020-02-24 00:00:00

abstract：:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...

journal_title：Journal of chemical information and modeling

authors： Batista KEA,Ocampo-Restrepo VK,Soares MD,Quiles MG,Piotrowski MJ,Da Silva JLF

更新日期：2020-02-24 00:00:00

abstract：:Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate-dependent enzyme involved in the biosynthesis of valine, leucine, isoleucine, and lysine. Experimental evidence has shown that mutation of the Gln202 residue results in a decrease in the enzymatic activity, thus suggesting the main role of the carboligation cat...

journal_title：Journal of chemical information and modeling

authors： Mendoza F,Medina FE,Jiménez VA,Jaña GA

更新日期：2020-02-24 00:00:00

abstract：:Moving to a new country, with a different culture and a new environment, is not an easy decision. In this perspective, I present some reasons that made me, a Brazilian computational biochemist, move abroad to do postdoctoral research and some of the challenges I faced before and after moving. ...

journal_title：Journal of chemical information and modeling

authors： Nunes-Alves A

更新日期：2020-02-24 00:00:00

abstract：:In the present contribution, we have developed a database, called the FAR-database, where the acronym FAR stands for Fused Aromatic Rings, which presents the results of nuclear independent chemical shifts calculations, NICS(0), NICS(1), NICS(0)ZZ, and NICS(1)ZZ, of 660 neutral benzenoid-PAHs and cyclopenta-fused PAHs....

journal_title：Journal of chemical information and modeling

authors： Alvarez-Ramírez F,Ruiz-Morales Y

更新日期：2020-02-24 00:00:00

abstract：:Protein-polysaccharide complexes constructed via self-assembly methods are often used to develop novel biomaterials for a wide range of applications in biomedicine, food, and biotechnology. The objective of this work was to investigate theoretically and to demonstrate via constant-pH Monte Carlo simulations that the c...

journal_title：Journal of chemical information and modeling

authors： Prudkin-Silva C,Pérez OE,Martínez KD,Barroso da Silva FL

更新日期：2020-02-24 00:00:00

abstract：:Over the last few decades, anticancer peptides (ACPs) have turned into potential warheads against cancer. Apart from small molecules and monoclonal antibodies, ACPs have been proven to be effective against cancer cells. ACPs are small cationic peptides that selectively bind to the negatively charged cancer cell membra...

journal_title：Journal of chemical information and modeling

authors： Singh M,Kumar V,Sikka K,Thakur R,Harioudh MK,Mishra DP,Ghosh JK,Siddiqi MI

更新日期：2020-01-27 00:00:00

abstract：:When both the difference between two quantities and their individual values can be measured or computationally predicted, multiple quantities can be determined from the measurements or predictions of select individual quantities and select pairwise differences. These measurements and predictions form a network connect...

journal_title：Journal of chemical information and modeling

authors： Xu H

更新日期：2019-11-25 00:00:00

abstract：:Discovery of new antibacterial agents is a never-ending task of medicinal chemistry. Every new drug brings significant improvement to patients with bacterial infections, but prolonged usage of antibacterials leads to the emergence of resistant strains. Therefore, novel active structures with new modes of action are re...

journal_title：Journal of chemical information and modeling

authors： Pogodin PV,Lagunin AA,Rudik AV,Druzhilovskiy DS,Filimonov DA,Poroikov VV

更新日期：2019-11-25 00:00:00

abstract：:Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacter...

journal_title：Journal of chemical information and modeling

authors： Husen P,Nielsen C,Martino CF,Solov'yov IA

更新日期：2019-11-25 00:00:00

abstract：:Structure-based virtual screening is highly used in the early stages of drug discovery to identify new putative lead compounds for a given target. However, when a small molecule elicits a biological effect, but its target is unknown, or the side effects it causes arise from its undesired interaction with unknown count...

journal_title：Journal of chemical information and modeling

authors： De Vita S,Lauro G,Ruggiero D,Terracciano S,Riccio R,Bifulco G

更新日期：2019-11-25 00:00:00

abstract：:Herein we present the VMD Store, an open-source VMD plugin that simplifies the way that users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism...

journal_title：Journal of chemical information and modeling

authors： Fernandes HS,Sousa SF,Cerqueira NMFSA

更新日期：2019-11-25 00:00:00

abstract：:Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical ...

journal_title：Journal of chemical information and modeling

authors： Zakharov AV,Zhao T,Nguyen DT,Peryea T,Sheils T,Yasgar A,Huang R,Southall N,Simeonov A

更新日期：2019-11-25 00:00:00

abstract：:Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to ...

journal_title：Journal of chemical information and modeling

authors： Abraham M,Apostolov R,Barnoud J,Bauer P,Blau C,Bonvin AMJJ,Chavent M,Chodera J,Čondić-Jurkić K,Delemotte L,Grubmüller H,Howard RJ,Jordan EJ,Lindahl E,Ollila OHS,Selent J,Smith DGA,Stansfeld PJ,Tiemann JKS,Trellet M

更新日期：2019-10-28 00:00:00

abstract：:As a key player in cell adhesion, the glycoprotein fibronectin is involved in the complex mechanobiology of the extracellular matrix. Although the function of many modules in the fibronectin molecule has already been understood, the structure and biological relevance of the C-terminal cross-linked region (CTXL) still ...

journal_title：Journal of chemical information and modeling

authors： Kulke M,Uhrhan M,Geist N,Brüggemann D,Ohler B,Langel W,Köppen S

更新日期：2019-10-28 00:00:00

abstract：:Solubility parameter models are widely used to select suitable solvents/nonsolvents for polymers in a variety of processing and engineering applications. In this study, we focus on two well-established models, namely, the Hildebrand and Hansen solubility parameter models. Both models are built on the basis of the noti...

journal_title：Journal of chemical information and modeling

authors： Venkatram S,Kim C,Chandrasekaran A,Ramprasad R

更新日期：2019-10-28 00:00:00

abstract：:FFAR4 has been considered as a potential target for metabolic diseases, including diabetes. Some compounds with biphenyl scaffold, represented by compound SR13 reported by our group, showed significant FFAR4 selectivity. However, the molecular basis for their selectivity has not been definitely disclosed. This study p...

journal_title：Journal of chemical information and modeling

authors： Zhang X,Sun H,Wen X,Yuan H

更新日期：2019-10-28 00:00:00

abstract：:This article presents the computation of both inter- and intramolecular hydrogen bond strengths from first-principles. Quantum chemical calculations conducted at the dispersion-corrected density functional theory level including free energy and solvation contributions are conducted for (i) one-to-one hydrogen-bonded c...

journal_title：Journal of chemical information and modeling

authors： Bauer CA

更新日期：2019-09-23 00:00:00

abstract：:Reaction databases provide a great deal of useful information to assist planning of experiments but do not provide any interpretation or chemical concepts to accompany this information. In this work, reactions are labeled with experimental conditions, and network analysis shows that consistencies within clusters of da...

journal_title：Journal of chemical information and modeling

authors： Walker E,Kammeraad J,Goetz J,Robo MT,Tewari A,Zimmerman PM

更新日期：2019-09-23 00:00:00

abstract：:We introduce the statistics behind a novel type of SAR analysis named "nonadditivity analysis". On the basis of all pairs of matched pairs within a given data set, the approach analyzes whether the same transformations between related molecules have the same effect, i.e., whether they are additive. Assuming that the e...

journal_title：Journal of chemical information and modeling

authors： Kramer C

更新日期：2019-09-23 00:00:00

abstract：:An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are...

journal_title：Journal of chemical information and modeling

authors： Ibrahim P,Wifling D,Clark T

更新日期：2019-09-23 00:00:00

abstract：:Small molecules targeting peripheral CB1 receptors have therapeutic potential in a variety of disorders including obesity-related, hormonal, and metabolic abnormalities, while avoiding the psychoactive effects in the central nervous system. We applied our in-house algorithm, iterative stochastic elimination, to produc...

journal_title：Journal of chemical information and modeling

authors： El-Atawneh S,Hirsch S,Hadar R,Tam J,Goldblum A

更新日期：2019-09-23 00:00:00

abstract：:The primary goal of this project was to evaluate the performance of the Standard and Enforced Geometry Optimization (SEGO) method which we have recently developed. The SEGO method has been designed for an automatic location of multiple minima on the molecular Potential Energy Surface (PES), and its usefulness has been...

journal_title：Journal of chemical information and modeling

authors： Brzyska A,Woliński K

更新日期：2019-08-26 00:00:00

abstract：:In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, natural products, agrochemicals, and cosmetics. FAME 3 was derived from the MetaQSAR database ( Pedre...

journal_title：Journal of chemical information and modeling

authors： Šícho M,Stork C,Mazzolari A,de Bruyn Kops C,Pedretti A,Testa B,Vistoli G,Svozil D,Kirchmair J

更新日期：2019-08-26 00:00:00

abstract：:Molecular dynamics simulations provide valuable insights into the behavior of molecular systems. Extending the recent trend of using machine learning techniques to predict physicochemical properties from molecular dynamics data, we propose to consider the trajectories as multidimensional time series represented by 2D ...

journal_title：Journal of chemical information and modeling

authors： Berishvili VP,Perkin VO,Voronkov AE,Radchenko EV,Syed R,Venkata Ramana Reddy C,Pillay V,Kumar P,Choonara YE,Kamal A,Palyulin VA

更新日期：2019-08-26 00:00:00

abstract：:The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the molecular docking algorithms used in structure-based drug discovery. To remedy this problem, elaborate rescoring and postprocessing schemes have been developed with a varying degree of success, specificity, ...

journal_title：Journal of chemical information and modeling

authors： Kurkinen ST,Lätti S,Pentikäinen OT,Postila PA

更新日期：2019-08-26 00:00:00