Isomerization and Decomposition of 2-Methylfuran with External Forces.

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 demonstrated so far for three molecules only. In this project we applied the SEGO method to explore the 2-methylfuran (2MF) PES. Our choice was not accidental: this molecule recently gained a great deal of interest as a potential candidate for biofuel, and therefore its pyrolysis is extensively studied. To understand pyrolysis of 2MF a detailed knowledge about its PES is needed. In these studies we explored the 2MF PES and located a surprisingly large number of local minima corresponding to 2MF isomers and decomposition products. Some of the 2MF isomers and fragments have amazing structures which most likely were previously unknown. All structures presented in this paper were found in an automatic manner as a result of the enforced chemical reactions driven by the SEGO method. Thus, in these studies we have not only proven that the SEGO method is a very efficient tool for exploring molecular potential energy surfaces, but we also obtained very detailed knowledge about the 2MF PES.

journal_name

J Chem Inf Model

authors

Brzyska A,Woliński K

doi

10.1021/acs.jcim.9b00352

subject

Has Abstract

pub_date

2019-08-26 00:00:00

pages

3454-3463

issue

8

eissn

1549-9596

issn

1549-960X

journal_volume

59

pub_type

杂志文章
  • Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory.

    abstract::The goal of the present study was to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling time. For this purpose, we selected the 16-mer peptide Bak16BH3 as a model for study and carri...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00347

    authors: Perez JJ,Tomas MS,Rubio-Martinez J

    更新日期:2016-10-24 00:00:00

  • Linear and nonlinear 3D-QSAR approaches in tandem with ligand-based homology modeling as a computational strategy to depict the pyrazolo-triazolo-pyrimidine antagonists binding site of the human adenosine A2A receptor.

    abstract::The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Sur...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700300w

    authors: Michielan L,Bacilieri M,Schiesaro A,Bolcato C,Pastorin G,Spalluto G,Cacciari B,Klotz KN,Kaseda C,Moro S

    更新日期:2008-02-01 00:00:00

  • Transplant-insert-constrain-relax-assemble (TICRA): protein-ligand complex structure modeling and application to kinases.

    abstract::We introduce TICRA (transplant-insert-constrain-relax-assemble), a method for modeling the structure of unknown protein-ligand complexes using the X-ray crystal structures of homologous proteins and ligands with known activity. We present results from modeling the structures of protein kinase-inhibitor complexes using...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100256u

    authors: Meshkat S,Klon AE,Zou J,Wiseman JS,Konteatis Z

    更新日期:2011-01-24 00:00:00

  • Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.

    abstract::Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explore...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00347

    authors: Aldeghi M,Bodkin MJ,Knapp S,Biggin PC

    更新日期:2017-09-25 00:00:00

  • GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking.

    abstract::Virtual screening is routinely used to discover new ligands and in particular new ligand chemotypes for G protein-coupled receptors (GPCRs). To prepare for a virtual screen, we often tailor a docking protocol that will enable us to select the best candidates for further screening. To aid this, we created GPCR-Bench, a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00660

    authors: Weiss DR,Bortolato A,Tehan B,Mason JS

    更新日期:2016-04-25 00:00:00

  • Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants.

    abstract::Previously, stereoselective hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N was observed. While both mutants hydroxylate α-ionone in a regioselective manner at the C3 position, M01 A82W catalyzes formation of trans-3-OH-α-ionone products whereas M11 L437N exhibits opposite stereoselecti...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300243n

    authors: de Beer SB,Venkataraman H,Geerke DP,Oostenbrink C,Vermeulen NP

    更新日期:2012-08-27 00:00:00

  • Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

    abstract::Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00235

    authors: Zhang Q,Xu Z,Shi J,Zhu W

    更新日期:2017-07-24 00:00:00

  • BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.

    abstract::In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc molecular dynamics protocols in a novel and task-oriented environment; as a notebook, BiKi (acronym of Binding Kinetics) keeps memory of any activity together with dependencies among...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00680

    authors: Decherchi S,Bottegoni G,Spitaleri A,Rocchia W,Cavalli A

    更新日期:2018-02-26 00:00:00

  • Exploring Tunable Hyperparameters for Deep Neural Networks with Industrial ADME Data Sets.

    abstract::Deep learning has drawn significant attention in different areas including drug discovery. It has been proposed that it could outperform other machine learning algorithms, especially with big data sets. In the field of pharmaceutical industry, machine learning models are built to understand quantitative structure-acti...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00671

    authors: Zhou Y,Cahya S,Combs SA,Nicolaou CA,Wang J,Desai PV,Shen J

    更新日期:2019-03-25 00:00:00

  • Predictive models for cytochrome p450 isozymes based on quantitative high throughput screening data.

    abstract::The human cytochrome P450 (CYP450) isozymes are the most important enzymes in the body to metabolize many endogenous and exogenous substances including environmental toxins and therapeutic drugs. Any unnecessary interactions between a small molecule and CYP450 isozymes may raise a potential to disarm the integrity of ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200311w

    authors: Sun H,Veith H,Xia M,Austin CP,Huang R

    更新日期:2011-10-24 00:00:00

  • How do metabolites differ from their parent molecules and how are they excreted?

    abstract::Understanding which physicochemical properties, or property distributions, are favorable for successful design and development of drugs, nutritional supplements, cosmetics, and agrochemicals is of great importance. In this study we have analyzed molecules from three distinct chemical spaces (i) approved drugs, (ii) hu...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300487z

    authors: Kirchmair J,Howlett A,Peironcely JE,Murrell DS,Williamson MJ,Adams SE,Hankemeier T,van Buren L,Duchateau G,Klaffke W,Glen RC

    更新日期:2013-02-25 00:00:00

  • Determining the validity of a QSAR model--a classification approach.

    abstract::The determination of the validity of a QSAR model when applied to new compounds is an important concern in the field of QSAR and QSPR modeling. Various scoring techniques can be applied to specific types of models. We present a technique with which we can state whether a new compound will be well predicted by a previo...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0497511

    authors: Guha R,Jurs PC

    更新日期:2005-01-01 00:00:00

  • Expert system for predicting reaction conditions: the Michael reaction case.

    abstract::A generic chemical transformation may often be achieved under various synthetic conditions. However, for any specific reagents, only one or a few among the reported synthetic protocols may be successful. For example, Michael β-addition reactions may proceed under different choices of solvent (e.g., hydrophobic, aproti...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500698a

    authors: Marcou G,Aires de Sousa J,Latino DA,de Luca A,Horvath D,Rietsch V,Varnek A

    更新日期:2015-02-23 00:00:00

  • DNA minor groove pharmacophores describing sequence specific properties.

    abstract::The more that is known about human and other genome sequences and the correlation between gene expression and the course of a disease, the more evident it seems to be that DNA is chosen as a drug target instead of proteins which are built with the information encoded by DNA. According to this approach, small minor gro...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600500v

    authors: Spitzer GM,Wellenzohn B,Laggner C,Langer T,Liedl KR

    更新日期:2007-07-01 00:00:00

  • Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b01138

    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

  • Concept-based semi-automatic classification of drugs.

    abstract::The anatomical therapeutic chemical (ATC) classification system maintained by the World Health Organization provides a global standard for the classification of medical substances and serves as a source for drug repurposing research. Nevertheless, it lacks several drugs that are major players in the global drug market...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci9000844

    authors: Gurulingappa H,Kolárik C,Hofmann-Apitius M,Fluck J

    更新日期:2009-08-01 00:00:00

  • BFMP: a method for discretizing and visualizing pyranose conformations.

    abstract::We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automate...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500325b

    authors: Makeneni S,Foley BL,Woods RJ

    更新日期:2014-10-27 00:00:00

  • Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation.

    abstract::One of the largest commercial applications of enzymes and surfactants is as main components in modern detergents. The high concentration of surfactant compounds usually present in detergents can, however, negatively affect the enzymatic activity. To remedy this drawback, it is of great importance to characterize the i...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00857

    authors: Kjølbye LR,Laustsen A,Vestergaard M,Periole X,De Maria L,Svendsen A,Coletta A,Schiøtt B

    更新日期:2019-05-28 00:00:00

  • FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00376

    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

  • Pharmer: efficient and exact pharmacophore search.

    abstract::Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tre...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200097m

    authors: Koes DR,Camacho CJ

    更新日期:2011-06-27 00:00:00

  • Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures.

    abstract::To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900068k

    authors: Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

    更新日期:2009-05-01 00:00:00

  • Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments.

    abstract::Docking into multiple receptor conformations ("ensemble docking") has been proposed, and employed, in the hope that it may account for receptor flexibility in virtual screening and thus provide higher enrichments than docking into single rigid receptor structures. The statistical analyses presented in this paper provi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900407c

    authors: Craig IR,Essex JW,Spiegel K

    更新日期:2010-04-26 00:00:00

  • Ligand binding determinants for angiotensin II type 1 receptor from computer simulations.

    abstract::The ligand binding determinants for the angiotensin II type 1 receptor (AT1R), a G protein-coupled receptor (GPCR), have been characterized by means of computer simulations. As a first step, a pharmacophore model of various known AT1R ligands exhibiting a wide range of binding affinities was generated. Second, a struc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400400m

    authors: Matsoukas MT,Cordomí A,Ríos S,Pardo L,Tselios T

    更新日期:2013-11-25 00:00:00

  • Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules.

    abstract::The Torsion Library contains hundreds of rules for small molecule conformations which have been derived from the Cambridge Structural Database (CSD) and are curated by molecular design experts. The torsion rules are encoded as SMARTS patterns and categorize rotatable bonds via a traffic light coloring scheme. We have ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00522

    authors: Guba W,Meyder A,Rarey M,Hert J

    更新日期:2016-01-25 00:00:00

  • Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.

    abstract::Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identif...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00398

    authors: Combs SA,Mueller BK,Meiler J

    更新日期:2018-05-29 00:00:00

  • Molecular Mechanism underlying PRMT1 Dimerization for SAM Binding and Methylase Activity.

    abstract::Protein arginine methyltransferases (PRMTs) catalyze the posttranslational methylation of arginine, which is important in a range of biological processes, including epigenetic regulation, signal transduction, and cancer progression. Although previous studies of PRMT1 mutants suggest that the dimerization arm and the N...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00454

    authors: Zhou R,Xie Y,Hu H,Hu G,Patel VS,Zhang J,Yu K,Huang Y,Jiang H,Liang Z,Zheng YG,Luo C

    更新日期:2015-12-28 00:00:00

  • How to Model Inter- and Intramolecular Hydrogen Bond Strengths with Quantum Chemistry.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00132

    authors: Bauer CA

    更新日期:2019-09-23 00:00:00

  • Random forest models to predict aqueous solubility.

    abstract::Random Forest regression (RF), Partial-Least-Squares (PLS) regression, Support Vector Machines (SVM), and Artificial Neural Networks (ANN) were used to develop QSPR models for the prediction of aqueous solubility, based on experimental data for 988 organic molecules. The Random Forest regression model predicted aqueou...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci060164k

    authors: Palmer DS,O'Boyle NM,Glen RC,Mitchell JB

    更新日期:2007-01-01 00:00:00

  • Prediction of pH-dependent aqueous solubility of druglike molecules.

    abstract::In the present work, the Henderson-Hasselbalch (HH) equation has been employed for the development of a tool for the prediction of pH-dependent aqueous solubility of drugs and drug candidates. A new prediction method for the intrinsic solubility was developed, based on artificial neural networks that have been trained...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600292q

    authors: Hansen NT,Kouskoumvekaki I,Jørgensen FS,Brunak S,Jónsdóttir SO

    更新日期:2006-11-01 00:00:00

  • Assessing the Protective Activity of a Recently Discovered Phenolic Compound against Oxidative Stress Using Computational Chemistry.

    abstract::The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times an...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00513

    authors: Villuendas-Rey Y,Alvarez-Idaboy JR,Galano A

    更新日期:2015-12-28 00:00:00