RED: a set of molecular descriptors based on Renyi entropy.

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：: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：:SIRT2, which is a NAD+ (nicotinamide adenine dinucleotide) dependent deacetylase, has been demonstrated to play an important role in the occurrence and development of a variety of diseases such as cancer, ischemia-reperfusion, and neurodegenerative diseases. Small molecule inhibitors of SIRT2 are thought to be potenti...

journal_title：Journal of chemical information and modeling

authors： Huang S,Song C,Wang X,Zhang G,Wang Y,Jiang X,Sun Q,Huang L,Xiang R,Hu Y,Li L,Yang S

更新日期：2017-04-24 00:00:00

abstract：:The reuptake of neurotransmitters by dopamine, norepinephrine, and serotonin transporters during neuronal transmission requires a sodium gradient. An "ionic mode" of binding proposes that aspartate anchors the ligand's positive charge but ignores the direct role of sodium in ligand binding seen in the only representat...

journal_title：Journal of chemical information and modeling

authors： Xhaard H,Backström V,Denessiouk K,Johnson MS

更新日期：2008-07-01 00:00:00

abstract：:Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...

journal_title：Journal of chemical information and modeling

authors： Xu L,Shan S,Chen Y,Wang X,Nussinov R,Ma B

更新日期：2015-06-22 00:00:00

abstract：:With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed ...

journal_title：Journal of chemical information and modeling

authors： Lee HS,Im W

更新日期：2012-10-22 00:00:00

abstract：:The in silico prediction of unwanted side effects (SEs) caused by the promiscuous behavior of drugs and their targets is highly relevant to the pharmaceutical industry. Considerable effort is now being put into computational and experimental screening of several suspected off-target proteins in the hope that SEs might...

journal_title：Journal of chemical information and modeling

authors： Pérez-Nueno VI,Souchet M,Karaboga AS,Ritchie DW

更新日期：2015-09-28 00:00:00

abstract：:In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initial...

journal_title：Journal of chemical information and modeling

authors： Delort B,Renault P,Charlier L,Raussin F,Martinez J,Floquet N

更新日期：2017-03-27 00:00:00

abstract：:The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used a...

journal_title：Journal of chemical information and modeling

authors： Kimand SK,Jacobson KA

更新日期：2007-05-01 00:00:00

abstract：:The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics...

journal_title：Journal of chemical information and modeling

authors： Wang M,Li P,Jia X,Liu W,Shao Y,Hu W,Zheng J,Brooks BR,Mei Y

更新日期：2017-10-23 00:00:00

abstract：:Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Curren...

journal_title：Journal of chemical information and modeling

authors： Ashtawy HM,Mahapatra NR

更新日期：2018-01-22 00:00:00

abstract：:Big data is one of the key transformative factors which increasingly influences all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: ...

journal_title：Journal of chemical information and modeling

authors： Schneider N,Fechner N,Landrum GA,Stiefl N

更新日期：2017-08-28 00:00:00

abstract：:Class II fructose-1,6-bisphosphate aldolases (FBA-II) are attractive new targets for the discovery of drugs to combat invasive fungal infection, because they are absent in animals and higher plants. Although several FBA-II inhibitors have been reported, none of these inhibitors exhibit antifungal effect so far. In thi...

journal_title：Journal of chemical information and modeling

authors： Han X,Zhu X,Hong Z,Wei L,Ren Y,Wan F,Zhu S,Peng H,Guo L,Rao L,Feng L,Wan J

更新日期：2017-06-26 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：:The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...

journal_title：Journal of chemical information and modeling

authors： Mallajosyula SS,Adams KM,Barchi JJ,MacKerell AD

更新日期：2013-05-24 00:00:00

abstract：:We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluct...

journal_title：Journal of chemical information and modeling

authors： Bolia A,Ozkan SB

更新日期：2016-04-25 00:00:00

abstract：:Finding a canonical ordering of the atoms in a molecule is a prerequisite for generating a unique representation of the molecule. The canonicalization of a molecule is usually accomplished by applying some sort of graph relaxation algorithm, the most common of which is the Morgan algorithm. There are known issues with...

journal_title：Journal of chemical information and modeling

authors： Schneider N,Sayle RA,Landrum GA

更新日期：2015-10-26 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：: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：: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

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

更新日期：2011-01-24 00:00:00

abstract：:Resistance remains a major issue with regards to HIV-1 protease, despite the availability of numerous HIV-1 protease inhibitors and copious amounts of structural and binding data. In an effort to improve our understanding of how HIV-1 protease is able to "outsmart" new drugs, we have investigated the flexibility of HI...

journal_title：Journal of chemical information and modeling

authors： Oehme DP,Wilson DJ,Brownlee RT

更新日期：2011-05-23 00:00:00

abstract：:Cytochrome P450 2D6 (CYP2D6) is used to develop an approach for predicting affinity and relevant binding conformation(s) for highly flexible binding sites. The approach combines the use of docking scores and compound properties as attributes in building a neural network (NN) model. It begins by identifying segments of...

journal_title：Journal of chemical information and modeling

authors： Bazeley PS,Prithivi S,Struble CA,Povinelli RJ,Sem DS

更新日期：2006-11-01 00:00:00

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

authors： Koes DR,Camacho CJ

更新日期：2011-06-27 00:00:00

abstract：:Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descr...

journal_title：Journal of chemical information and modeling

authors： Yilancioglu K,Weinstein ZB,Meydan C,Akhmetov A,Toprak I,Durmaz A,Iossifov I,Kazan H,Roth FP,Cokol M

更新日期：2014-08-25 00:00:00

abstract：:Metal-ligand (M-L) bond lengths for a range of ligands (carboxylates, chlorides, pyridines, water, tertiary phosphines, and alkenes) and a variety of metals have been retrieved from the Cambridge Structural Database, CSD. Analysis of the factors which affect M-L bond lengths (for example, ligand coordination mode, oxi...

journal_title：Journal of chemical information and modeling

authors： Harris SE,Orpen AG,Bruno IJ,Taylor R

更新日期：2005-11-01 00:00:00

abstract：:This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...

journal_title：Journal of chemical information and modeling

authors： Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

更新日期：2007-07-01 00:00:00

abstract：:Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of r...

journal_title：Journal of chemical information and modeling

authors： Gilis D,Biot C,Buisine E,Dehouck Y,Rooman M

更新日期：2006-03-01 00:00:00

abstract：:The membrane permeability of cyclic peptides and peptidomimetics, which are generally larger and more complex than typical drug molecules, is likely strongly influenced by the conformational behavior of these compounds in polar and apolar environments. The size and complexity of peptides often limit their bioavailabil...

journal_title：Journal of chemical information and modeling

authors： Witek J,Keller BG,Blatter M,Meissner A,Wagner T,Riniker S

更新日期：2016-08-22 00:00:00

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

authors： Craig IR,Essex JW,Spiegel K

更新日期：2010-04-26 00:00:00

abstract：:A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...

journal_title：Journal of chemical information and modeling

authors： Agrafiotis DK,Bandyopadhyay D,Farnum M

更新日期：2007-01-01 00:00:00