Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matrices.

abstract：:Binding affinity prediction with implicit solvent models remains a challenge in virtual screening for drug discovery. In order to assess the predictive power of implicit solvent models in docking techniques with Amber scoring, three generalized Born models (GBHCT, GBOBCI, and GBOBCII) available in Dock 6.7 were utiliz...

journal_title：Journal of chemical information and modeling

authors： Zhang H,Yin C,Yan H,van der Spoel D

更新日期：2016-10-24 00:00:00

abstract：:Piperine, the bioactive phytochemical from black pepper (Piper nigrum L.), is a nontoxic natural compound exhibiting many physiological and pharmacological properties. They include antioxidant, anti-inflammatory, antimutagenic, antitumor, antiapoptotic, antigenotoxic, antiarthritic, antifungal, antimicrobial, antidepr...

journal_title：Journal of chemical information and modeling

authors： Haris P,Mary V,Haridas M,Sudarsanakumar C

更新日期：2015-12-28 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：:Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its h...

journal_title：Journal of chemical information and modeling

authors： Machireddy B,Kalra G,Jonnalagadda S,Ramanujachary K,Wu C

更新日期：2017-11-27 00:00:00

abstract：:In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimen...

journal_title：Journal of chemical information and modeling

authors： Zhang T,Sharma G,Paul TJ,Hoffmann Z,Prabhakar R

更新日期：2017-05-22 00:00:00

abstract：:We used synthetic peloruside A for the commercial preparation of [³H]peloruside A. The radiolabeled compound bound to preformed tubulin polymer in amounts stoichiometric with the polymer's tubulin content, with an apparent K(d) value of 0.35 μM. A less active peloruside A analogue, (11-R)-peloruside A and laulimalide ...

journal_title：Journal of chemical information and modeling

authors： Nguyen TL,Xu X,Gussio R,Ghosh AK,Hamel E

更新日期：2010-11-22 00:00:00

abstract：:The predictive performances of MC4PC were evaluated using its learning machine functionality. Its superior characteristics are demonstrated in this following up study using the newly published Ames mutagenicity benchmark set. ...

journal_title：Journal of chemical information and modeling

authors： Saiakhov RD,Klopman G

更新日期：2010-09-27 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：:Mapping the chemical space of small organic molecules is approached from a theoretical graph theory viewpoint, in an effort to begin the systematic exploration of molecular topologies. We present an algorithm for exhaustive generation of scaffold topologies with up to eight rings and an efficient comparison method for...

journal_title：Journal of chemical information and modeling

authors： Pollock SN,Coutsias EA,Wester MJ,Oprea TI

更新日期：2008-07-01 00:00:00

abstract：:We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which kn...

journal_title：Journal of chemical information and modeling

authors： Huang N,Kalyanaraman C,Irwin JJ,Jacobson MP

更新日期：2006-01-01 00:00:00

abstract：:The causative agent of African sleeping sickness, Trypanosoma brucei , undergoes an unusual mitochondrial RNA editing process that is essential for its survival. RNA editing terminal uridylyl transferase 2 of T. brucei (TbRET2) is an indispensable component of the editosome machinery that performs this editing. TbR...

journal_title：Journal of chemical information and modeling

authors： Demir Ö,Amaro RE

更新日期：2012-05-25 00:00:00

abstract：:Taking into account dynamical behavior and/or structural inaccuracies of receptor-ligand systems becomes increasingly important in structure-based drug design. Here, we describe the development of consensus Adaptation of Fields for Molecular Comparison (AFMoC) (abbreviated as AFMoCcon) models that account for multiple...

journal_title：Journal of chemical information and modeling

authors： Breu B,Silber K,Gohlke H

更新日期：2007-11-01 00:00:00

abstract：:Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the ob...

journal_title：Journal of chemical information and modeling

authors： Kalyaanamoorthy S,Chen YP

更新日期：2012-02-27 00:00:00

abstract：:The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have be...

journal_title：Journal of chemical information and modeling

authors： Klamt A,Thormann M,Wichmann K,Tosco P

更新日期：2012-08-27 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：: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：:The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with b...

journal_title：Journal of chemical information and modeling

authors： Hansen MR,Villar HO,Feyfant E

更新日期：2013-10-28 00:00:00

abstract：:An essential feature of all practical de novo molecule generating programs is the ability to focus the potential combinatorial explosion of grown molecules on a desired chemical space. It is a daunting task to balance the generation of new molecules with limitations on growth that produce desired features such as stab...

journal_title：Journal of chemical information and modeling

authors： Kutchukian PS,Lou D,Shakhnovich EI

更新日期：2009-07-01 00:00:00

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

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

abstract：:Sterol 14α-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The discovery of new efficient fungal CYP51 inhibitors requires an understanding of the structural requirements for selectivity for the fungal over the human ortholog. In this study, a binding mode of the pyridylethanol(phen...

journal_title：Journal of chemical information and modeling

authors： Zelenko U,Hodošček M,Rozman D,Golič Grdadolnik S

更新日期：2014-12-22 00:00:00

abstract：:Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coord...

journal_title：Journal of chemical information and modeling

authors： Lexa KW,Carlson HA

更新日期：2013-02-25 00:00:00

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

authors： Zhang Q,Xu Z,Shi J,Zhu W

更新日期：2017-07-24 00:00:00

abstract：:Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules ...

journal_title：Journal of chemical information and modeling

authors： Kogej T,Engkvist O,Blomberg N,Muresan S

更新日期：2006-05-01 00:00:00

abstract：:We have applied the two most commonly used methods for automatic matched pair identification, obtained the optimum settings, and discovered that the two methods are synergistic. A turbocharging approach to matched pair analysis is advocated in which a first round (a conservative categorical approach that uses an analo...

journal_title：Journal of chemical information and modeling

authors： Lukac I,Zarnecka J,Griffen EJ,Dossetter AG,St-Gallay SA,Enoch SJ,Madden JC,Leach AG

更新日期：2017-10-23 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：:Engineering shape-controlled bionanomaterials requires comprehensive understanding of interactions between biomolecules and inorganic surfaces. We explore the origin of facet-selective binding of peptides adsorbed onto Pt(100) and Pt(111) crystallographic planes. Using molecular dynamics simulations, we show that upon...

journal_title：Journal of chemical information and modeling

authors： Ramakrishnan SK,Martin M,Cloitre T,Firlej L,Cuisinier FJ,Gergely C

更新日期：2013-12-23 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：:Searching chemical databases for possible drug leads is often one of the main activities conducted during the early stages of a drug development project. This article shows that spherical harmonic molecular shape representations provide a powerful way to search and cluster small-molecule databases rapidly and accurate...

journal_title：Journal of chemical information and modeling

authors： Mavridis L,Hudson BD,Ritchie DW

更新日期：2007-09-01 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

abstract：:We describe a general methodology for designing an empirical scoring function and provide smina, a version of AutoDock Vina specially optimized to support high-throughput scoring and user-specified custom scoring functions. Using our general method, the unique capabilities of smina, a set of default interaction terms ...

journal_title：Journal of chemical information and modeling

authors： Koes DR,Baumgartner MP,Camacho CJ

更新日期：2013-08-26 00:00:00