abstract：:Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are th...

journal_title：Journal of chemical information and modeling

authors： Gong W,Liu Y,Zhao Y,Wang S,Han Z,Li C

更新日期：2021-01-26 00:00:00

abstract：:Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched de...

journal_title：Journal of chemical information and modeling

authors： Stein RM,Yang Y,Balius TE,O'Meara MJ,Lyu J,Young J,Tang K,Shoichet BK,Irwin JJ

更新日期：2021-01-25 00:00:00

abstract：:Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is im...

journal_title：Journal of chemical information and modeling

authors： Wu FX,Yang JF,Mei LC,Wang F,Hao GF,Yang GF

更新日期：2021-01-25 00:00:00

abstract：:The α2a adrenoceptor is a medically relevant subtype of the G protein-coupled receptor family. Unfortunately, high-throughput techniques aimed at producing novel drug leads for this receptor have been largely unsuccessful because of the complex pharmacology of adrenergic receptors. As such, cutting-edge in silico liga...

journal_title：Journal of chemical information and modeling

authors： Schultz KJ,Colby SM,Lin VS,Wright AT,Renslow RS

更新日期：2021-01-25 00:00:00

abstract：:Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic coupling...

journal_title：Journal of chemical information and modeling

authors： Aggarwal A,Vinayak V,Bag S,Bhattacharyya C,Waghmare UV,Maiti PK

更新日期：2021-01-25 00:00:00

abstract：:Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, w...

journal_title：Journal of chemical information and modeling

authors： Borkotoky S,Dey D,Banerjee M

更新日期：2021-01-25 00:00:00

abstract：:A machine learning enhanced spectrum recognition system called spectrum recognition based on computer vision (SRCV) for data extraction from previously analyzed 13C and 1H NMR spectra has been developed. The intelligent system was designed with four function modules to extract data from three areas of NMR images, incl...

journal_title：Journal of chemical information and modeling

authors： Jia W,Yang Z,Yang M,Cheng L,Lei Z,Wang X

更新日期：2021-01-25 00:00:00

abstract：:Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a co...

journal_title：Journal of chemical information and modeling

authors： Shahraki A,Işbilir A,Dogan B,Lohse MJ,Durdagi S,Birgul-Iyison N

更新日期：2021-01-21 00:00:00

abstract：:Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature o...

journal_title：Journal of chemical information and modeling

authors： Sun Y,Huang J,Duan X,Ding F

更新日期：2021-01-14 00:00:00

abstract：:Umami or the taste of monosodium glutamate represents one of the major attractive taste modalities in humans. Therefore, knowledge about biophysical and biochemical properties of the umami taste is important for both scientific research and the food industry. Experimental approaches for predicting umami peptides are l...

journal_title：Journal of chemical information and modeling

authors： Charoenkwan P,Yana J,Nantasenamat C,Hasan MM,Shoombuatong W

更新日期：2020-12-28 00:00:00

abstract：:Side-chain modeling is critical for protein structure prediction since the uniqueness of the protein structure is largely determined by its side-chain packing conformation. In this paper, differing from most approaches that rely on rotamer library sampling, we first propose a novel side-chain rotamer prediction method...

journal_title：Journal of chemical information and modeling

authors： Xu G,Wang Q,Ma J

更新日期：2020-12-28 00:00:00

abstract：:Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

journal_title：Journal of chemical information and modeling

authors： Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

更新日期：2020-12-28 00:00:00

abstract：:Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most wid...

journal_title：Journal of chemical information and modeling

authors： Rusu VH,Santos DES,Poleto MD,Galheigo MM,Gomes ATA,Verli H,Soares TA,Lins RD

更新日期：2020-12-28 00:00:00

abstract：:With continually increased computer power, molecular mechanics force field-based approaches, such as the endpoint methods of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA), have been routinely applied in both drug lead identification and opt...

journal_title：Journal of chemical information and modeling

authors： Hao D,He X,Ji B,Zhang S,Wang J

更新日期：2020-12-28 00:00:00

abstract：:Flavins are versatile biological cofactors which catalyze proton-coupled electron transfers (PCET) with varying number and coupling of electrons. Flavin-mediated oxidations of nicotinamide adenine dinucleotide (NADH) and of succinate, initial redox reactions in cellular respiration, were examined here with multiconfig...

journal_title：Journal of chemical information and modeling

authors： Curtolo F,Arantes GM

更新日期：2020-12-28 00:00:00

abstract：:The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CA...

journal_title：Journal of chemical information and modeling

authors： Prabhakant A,Panigrahi A,Krishnan M

更新日期：2020-12-28 00:00:00

abstract：:Derivation of structure-kinetics relationships can help rational design and development of new small-molecule drug candidates with desired residence times. Efforts are now being directed toward the development of efficient computational methods. Currently, there is a lack of solid, high-throughput binding kinetics pre...

journal_title：Journal of chemical information and modeling

authors： Amangeldiuly N,Karlov D,Fedorov MV

更新日期：2020-12-28 00:00:00

abstract：:Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochemical efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and t...

journal_title：Journal of chemical information and modeling

authors： Mihalovits LM,Ferenczy GG,Keserű GM

更新日期：2020-12-28 00:00:00

abstract：:Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but h...

journal_title：Journal of chemical information and modeling

authors： Lautala S,Provenzani R,Koivuniemi A,Kulig W,Talman V,Róg T,Tuominen RK,Yli-Kauhaluoma J,Bunker A

更新日期：2020-11-23 00:00:00

abstract：:Reduction of the affinity of the fragment crystallizable (Fc) region with immune receptors by substitution of one or a few amino acids, known as Fc-silencing, is an established approach to reduce the immune effector functions of monoclonal antibody therapeutics. This approach to Fc-silencing, however, is problematic a...

journal_title：Journal of chemical information and modeling

authors： Lešnik S,Hodošček M,Podobnik B,Konc J

更新日期：2020-11-23 00:00:00

abstract：:The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dynamics (MD) simulations of αvβ6 in complex with its natural ligand, pr...

journal_title：Journal of chemical information and modeling

authors： Guest EE,Oatley SA,Macdonald SJF,Hirst JD

更新日期：2020-11-23 00:00:00

abstract：:Deep learning has demonstrated significant potential in advancing state of the art in many problem domains, especially those benefiting from automated feature extraction. Yet, the methodology has seen limited adoption in the field of ligand-based virtual screening (LBVS) as traditional approaches typically require lar...

journal_title：Journal of chemical information and modeling

authors： Stojanović L,Popović M,Tijanić N,Rakočević G,Kalinić M

更新日期：2020-10-26 00:00:00

abstract：:Drug-induced torsade de pointes (TdP) is a life-threatening ventricular arrhythmia responsible for the withdrawal of many drugs from the market. Although currently used TdP risk-assessment methods are effective, they are expensive and prone to produce false positives. In recent years, in silico cardiac simulations hav...

journal_title：Journal of chemical information and modeling

authors： Llopis-Lorente J,Gomis-Tena J,Cano J,Romero L,Saiz J,Trenor B

更新日期：2020-10-26 00:00:00

abstract：:Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to...

journal_title：Journal of chemical information and modeling

authors： Burggraaff L,van Veen A,Lam CC,van Vlijmen HWT,IJzerman AP,van Westen GJP

更新日期：2020-10-26 00:00:00

abstract：:Artificial intelligence and multiobjective optimization represent promising solutions to bridge chemical and biological landscapes by addressing the automated de novo design of compounds as a result of a humanlike creative process. In the present study, we conceived a novel pair-based multiobjective approach implement...

journal_title：Journal of chemical information and modeling

authors： Domenico A,Nicola G,Daniela T,Fulvio C,Nicola A,Orazio N

更新日期：2020-10-26 00:00:00

abstract：:There are only four derivatives of pseudouridine (Ψ) that are known to occur naturally in RNA as post-transcriptional modifications. We have studied the conformational consequences of pseudouridylation and further modifications using replica exchange molecular dynamics simulations at the nucleoside level, and the simu...

journal_title：Journal of chemical information and modeling

authors： Dutta N,Sarzynska J,Lahiri A

更新日期：2020-10-26 00:00:00

abstract：:G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, which is arguably the most important family of drug target. With the technology breakthroughs in X-ray crystallography and cryo-electron microscopy, more than 300 GPCR-ligand complex structures have been publicly reported since 2007,...

journal_title：Journal of chemical information and modeling

authors： Li Y,Sun Y,Song Y,Dai D,Zhao Z,Zhang Q,Zhong W,Hu LA,Ma Y,Li X,Wang R

更新日期：2020-09-28 00:00:00

abstract：:The important role of water molecules in protein-ligand binding energetics has attracted wide attention in recent years. A range of computational methods has been developed to predict the favorable locations of water molecules in a protein binding pocket. Most of the current methods are based on extensive molecular dy...

journal_title：Journal of chemical information and modeling

authors： Li Y,Gao Y,Holloway MK,Wang R

更新日期：2020-09-28 00:00:00

abstract：:G-protein-coupled receptors (GPCRs) transmit signals into the cell in response to ligand binding at its extracellular domain, which is characterized by the coupling of agonist-induced receptor conformational change to guanine nucleotide (GDP) exchange with guanosine triphosphate on a heterotrimeric (αβγ) guanine nucle...

journal_title：Journal of chemical information and modeling

authors： Kumar V,Hoag H,Sader S,Scorese N,Liu H,Wu C

更新日期：2020-08-24 00:00:00

abstract：:The emergence of a large amount of pharmacological, genomic, and network knowledge data provides new challenges and opportunities for drug discovery and development. Identification of real small-molecule drug (SM)-miRNA associations is not only important in the development of effective drug repositioning but also cruc...

journal_title：Journal of chemical information and modeling

authors： Shen C,Luo J,Lai Z,Ding P

更新日期：2020-08-24 00:00:00

abstract：:Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimo...

journal_title：Journal of chemical information and modeling

authors： Siwy CM,Delfing BM,Smith AK,Klimov DK

更新日期：2020-08-24 00:00:00

abstract：:We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF...

journal_title：Journal of chemical information and modeling

authors： Istyastono EP,Radifar M,Yuniarti N,Prasasty VD,Mungkasi S

更新日期：2020-08-24 00:00:00

abstract：:Databases of small, potentially bioactive molecules are ubiquitous across the industry and academia. Designed such that each unique compound should appear only once, the multiplicity of ways in which many compounds can be represented means that these databases require methods for standardizing the representation of ch...

journal_title：Journal of chemical information and modeling

authors： Baker CM,Kidley NJ,Papachristos K,Hotson M,Carson R,Gravestock D,Pouliot M,Harrison J,Dowling A

更新日期：2020-08-24 00:00:00

abstract：:The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in sili...

journal_title：Journal of chemical information and modeling

authors： Zhang Y,Zhang HX,Zheng QC

更新日期：2020-07-27 00:00:00

abstract：:As an important member of cytochrome P450 (CYP) enzymes, CYP17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones, making it an attractive therapeutic target. The emerging structural information about CYP17A1 and the growing number of inhibitors for these enzymes ca...

journal_title：Journal of chemical information and modeling

authors： Xiao F,Song X,Tian P,Gan M,Verkhivker GM,Hu G

更新日期：2020-07-27 00:00:00

abstract：:Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class...

journal_title：Journal of chemical information and modeling

authors： Bergant Loboda K,Janežič M,Štampar M,Žegura B,Filipič M,Perdih A

更新日期：2020-07-27 00:00:00

abstract：:Advances in computer-aided translation technology have made tremendous progress in accuracy in the past few years. Chemical Abstracts Service of the American Chemical Society summarizes scientific works from more than 50 languages and allows the users to search papers in nine selected languages. Currently, only the ab...

journal_title：Journal of chemical information and modeling

authors： Wahab MF,Zulfiqar S,Sarwar MI,Lieberwirth I

更新日期：2020-07-27 00:00:00

abstract：:The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development, represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key ste...

journal_title：Journal of chemical information and modeling

authors： Hassan-Harrirou H,Zhang C,Lemmin T

更新日期：2020-06-22 00:00:00

abstract：:Generation and prioritization of new molecules are the most central part of the drug design process. Matched molecular series analysis (MMSA) has recently been proposed as a formal approach that captures both of these key elements of design. In order to better understand the power of MMSA and its specific limitations,...

journal_title：Journal of chemical information and modeling

authors： Awale M,Riniker S,Kramer C

更新日期：2020-06-22 00:00:00

abstract：:A giant technological leap in the field of cryo-electron microscopy (cryo-EM) has assured the achievement of near-atomic resolution structures of biological macromolecules. As a recognition of this accomplishment, the Nobel Prize in Chemistry was awarded in 2017 to Jacques Dubochet, Joachim Frank, and Richard Henderso...

journal_title：Journal of chemical information and modeling

authors： Akbar S,Mozumder S,Sengupta J

更新日期：2020-05-26 00:00:00