ColBioS-FlavRC: a collection of bioselective flavonoids and related compounds filtered from high-throughput screening outcomes.

abstract：:Saturated acyclic alkanes show steric strain if they are highly branched and, in extreme cases, fall apart rapidly at room temperature. Consequently, attempts to count the number of isomeric forms for a given molecular formula that neglect this physical consideration will inevitably overestimate the size of the availa...

journal_title：Journal of chemical information and modeling

authors： Paton RS,Goodman JM

更新日期：2007-11-01 00:00:00

abstract：:A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segme...

journal_title：Journal of chemical information and modeling

authors： Nagy G,Oostenbrink C

更新日期：2014-01-27 00:00:00

abstract：:We present an algorithm, ReFlex3D, for the refinement of flexible molecular alignments based on their three-dimensional shape and electrostatic properties. The algorithm is designed to be used with fast conformer generators to refine an initial overlay between two molecules and thus to obtain improved overlaps as judg...

journal_title：Journal of chemical information and modeling

authors： Schmidt TC,Cosgrove DA,Boström J

更新日期：2018-04-23 00:00:00

abstract：:We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...

journal_title：Journal of chemical information and modeling

authors： Borstnik U,Janezic D

更新日期：2005-11-01 00:00:00

abstract：:The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input stru...

journal_title：Journal of chemical information and modeling

authors： Feher M,Williams CI

更新日期：2009-07-01 00:00:00

abstract：:Representative molecules from 10 classes of prohibited substances were taken from the World Anti-Doping Agency (WADA) list, augmented by molecules from corresponding activity classes found in the MDDR database. Together with some explicitly allowed compounds, these formed a set of 5245 molecules. Five types of fingerp...

journal_title：Journal of chemical information and modeling

authors： Cannon EO,Bender A,Palmer DS,Mitchell JB

更新日期：2006-11-01 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：: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：:An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of severa...

journal_title：Journal of chemical information and modeling

authors： Ombrato R,Cazzolla N,Mancini F,Mangano G

更新日期：2015-12-28 00:00:00

abstract：:The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to char...

journal_title：Journal of chemical information and modeling

authors： Otaki JM,Tsutsumi M,Gotoh T,Yamamoto H

更新日期：2010-04-26 00:00:00

abstract：:The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later...

journal_title：Journal of chemical information and modeling

authors： Kang H,Sheng Z,Zhu R,Huang Q,Liu Q,Cao Z

更新日期：2012-03-26 00:00:00

abstract：:G-protein coupled receptors (GPCRs) are highly relevant drug targets. Four GPCRs with known crystal structure were analyzed with docking (AutoDock4) and postdocking (MM-PBSA) in order to evaluate the ability to recognize known antagonists from a larger database of molecular decoys and to predict correct binding modes....

journal_title：Journal of chemical information and modeling

authors： Anighoro A,Rastelli G

更新日期：2013-04-22 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：:Alanine scanning is a tool in molecular biology that is commonly used to evaluate the contribution of a specific amino acid residue to the stability and function of a protein. Additionally, this tool is also used to understand whether the side chain of a specific amino acid residue plays a role in the protein's bioact...

journal_title：Journal of chemical information and modeling

authors： Coskuner-Weber O,Uversky VN

更新日期：2019-02-25 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：: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：:On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...

journal_title：Journal of chemical information and modeling

authors： Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

更新日期：2015-06-22 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：:A model for prediction of percent intestinal absorption (%Abs) of neutral molecules was developed based upon surface charges of the molecule calculated by density functional theory (DFT). The surface charges are decomposed into sigma moments which are correlated to a partition coefficient representing transfer of the ...

journal_title：Journal of chemical information and modeling

authors： Jones R,Connolly PC,Klamt A,Diedenhofen M

更新日期：2005-09-01 00:00:00

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

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

更新日期：2013-11-25 00:00:00

abstract：:TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad ...

journal_title：Journal of chemical information and modeling

authors： Ghysels A,Verstraelen T,Hemelsoet K,Waroquier M,Van Speybroeck V

更新日期：2010-09-27 00:00:00

abstract：:The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemica...

journal_title：Journal of chemical information and modeling

authors： Sameera WMC,Maseras F

更新日期：2018-09-24 00:00:00

abstract：:Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular a...

journal_title：Journal of chemical information and modeling

authors： Brown BP,Mendenhall J,Meiler J

更新日期：2019-02-25 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：:Optimization of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly because of its lack of accuracy and reproducibili...

journal_title：Journal of chemical information and modeling

authors： Wan S,Bhati AP,Skerratt S,Omoto K,Shanmugasundaram V,Bagal SK,Coveney PV

更新日期：2017-04-24 00:00:00

abstract：:Ionotropic glutamate receptors (iGluRs) are synaptic proteins that facilitate signal transmission in the central nervous system. Extracellular iGluR cleft closure is linked to receptor activation; however, the mechanism underlying partial agonism is not entirely understood. Full agonists close the bilobed ligand-bindi...

journal_title：Journal of chemical information and modeling

authors： Postila PA,Ylilauri M,Pentikäinen OT

更新日期：2011-05-23 00:00:00

abstract：:We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assemb...

journal_title：Journal of chemical information and modeling

authors： Kang M,Chakraborty K,Loverde SM

更新日期：2018-06-25 00:00:00

abstract：:A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper ...

journal_title：Journal of chemical information and modeling

authors： Andersson CR,Fryknäs M,Rickardson L,Larsson R,Isaksson A,Gustafsson MG

更新日期：2007-01-01 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：: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