Efficient overlay of small organic molecules using 3D pharmacophores.

abstract：:Computational techniques, such as Quantitative Structure-Property Relationship (QSPR) modeling, are very useful in predicting physicochemical properties of various chemicals. Building QSPR models requires calculating molecular descriptors and the proper choice of the geometry optimization method, which will be dedicat...

journal_title：Journal of computer-aided molecular design

authors： Rybinska A,Sosnowska A,Barycki M,Puzyn T

更新日期：2016-02-01 00:00:00

abstract：:The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-l...

journal_title：Journal of computer-aided molecular design

authors： Albada HB,Golub E,Willner I

更新日期：2015-07-01 00:00:00

abstract：:The Ligand Design (LUDI) approach has been used in order to design leucine aminopeptidase inhibitors, predict their activity and analyze their interactions with the enzyme. The investigation was based on the crystal structure of bovine lens leucine aminopeptidase (LAP) complexed with its inhibitor--the phosphonic acid...

journal_title：Journal of computer-aided molecular design

authors： Grembecka J,Sokalski WA,Kafarski P

更新日期：2000-08-01 00:00:00

abstract：:Drug discovery is an expensive and time-consuming process. To make this process more efficient quantum chemistry methods can be employed. The electrophilicity index is one property that can be calculated by quantum chemistry methods, and if calculated correctly gives insight into the reactivity of covalent inhibitors....

journal_title：Journal of computer-aided molecular design

authors： Hermann MR,Pautsch A,Grundl MA,Weber A,Tautermann CS

更新日期：2020-10-05 00:00:00

abstract：:In the context of the SAMPL7 challenge, we computed, employing a non-equilibrium (NE) alchemical technique, the standard binding free energy of two series of host-guest systems, involving as a host the Isaac's TrimerTrip, a Cucurbituril-like open cavitand, and the Gilson's Cyclodextrin derivatives. The adopted NE alch...

journal_title：Journal of computer-aided molecular design

authors： Procacci P,Guarnieri G

更新日期：2021-01-04 00:00:00

abstract：:We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman an...

journal_title：Journal of computer-aided molecular design

authors： de Souza ON,Goodfellow JM

更新日期：1994-06-01 00:00:00

abstract：:Although auxins were the first type of plant hormone to be identified, little is known about the molecular mechanism of this important class of plant hormones. We present a classification of a set of about 50 compounds with measured auxin activities, according to their interaction properties. Four classes of compounds...

journal_title：Journal of computer-aided molecular design

authors： Tomić S,Gabdoulline RR,Kojić-Prodić B,Wade RC

更新日期：1998-01-01 00:00:00

abstract：:This paper describes several case studies concerning protein function inference from its structure using our novel approach described in the accompanying paper. This approach employs family-specific motifs, i.e. three-dimensional amino acid packing patterns that are statistically prevalent within a protein family. For...

journal_title：Journal of computer-aided molecular design

authors： Bandyopadhyay D,Huan J,Prins J,Snoeyink J,Wang W,Tropsha A

更新日期：2009-11-01 00:00:00

abstract：:Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incor...

journal_title：Journal of computer-aided molecular design

authors： Cramer CJ,Truhlar DG

更新日期：1992-12-01 00:00:00

abstract：:SIRT1 is an NAD+-dependent deacetylase, whose activators have potential therapeutic applications in the age-related, metabolic, neurode-generative and cardiovascular diseases. Resveratrol (RSV) has been regarded as potent SIRT1 activator in the treatment of atherosclerosis and cardiovascular diseases. Moreover, the pr...

journal_title：Journal of computer-aided molecular design

authors： Chen H,Wang Y,Gao Z,Yang W,Gao J

更新日期：2019-04-01 00:00:00

abstract：:Targeting Proviral integration-site of murine Moloney leukemia virus 1 kinase, hereafter called Pim-1 kinase, is a promising strategy for treating different kinds of human cancer. Headed for this a total list of 328 formerly reported Pim-1 kinase inhibitors has been explored and divided based on the pharmacophoric fea...

journal_title：Journal of computer-aided molecular design

authors： Shahin R,Swellmeen L,Shaheen O,Aboalhaija N,Habash M

更新日期：2016-01-01 00:00:00

abstract：:In the absence of a 3D structure of the target biomolecule, to propose the 3D requirements for a small molecule to exhibit a particular bioactivity, one must supply both a bioactive conformation and a superposition rule for every active compound. Our strategy identifies both simultaneously. We first generate and optim...

journal_title：Journal of computer-aided molecular design

authors： Martin YC,Bures MG,Danaher EA,DeLazzer J,Lico I,Pavlik PA

更新日期：1993-02-01 00:00:00

abstract：:G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur...

journal_title：Journal of computer-aided molecular design

authors： Campagne F,Jestin R,Reversat JL,Bernassau JM,Maigret B

更新日期：1999-11-01 00:00:00

abstract：:Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze da...

journal_title：Journal of computer-aided molecular design

authors： Raschka S,Wolf AJ,Bemister-Buffington J,Kuhn LA

更新日期：2018-04-01 00:00:00

abstract：:We have developed quantitative structure-activity relationship (QSAR) models for 44 non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type. The k nearest neighbor (kNN) variable selection approach was used. This method utilizes multiple descriptors such as molecular connectivi...

journal_title：Journal of computer-aided molecular design

authors： Medina-Franco JL,Golbraikh A,Oloff S,Castillo R,Tropsha A

更新日期：2005-04-01 00:00:00

abstract：:Cytochrome P450 (CYP) enzymes play an important role in the metabolism of xenobiotics. Since they are connected to drug interactions, screening for potential inhibitors is of utmost importance in drug discovery settings. Our study provides an extensive classification model for P450-drug interactions with one of the mo...

journal_title：Journal of computer-aided molecular design

authors： Rácz A,Keserű GM

更新日期：2020-08-01 00:00:00

abstract：:In order to identify novel chemical classes of factor Xa inhibitors, five scoring functions (FlexX, DOCK, GOLD, ChemScore and PMF) were engaged to evaluate the multiple docking poses generated by FlexX. The compound collection was composed of confirmed potent factor Xa inhibitors and a subset of the LeadQuest screenin...

journal_title：Journal of computer-aided molecular design

authors： Xing L,Hodgkin E,Liu Q,Sedlock D

更新日期：2004-05-01 00:00:00

abstract：:4-(Phenylamino)-pyrrolo[2,1-f][1,2,4]triazines have been discovered as inhibitors of p38alpha. Experimental assays have proven that the configuration of alpha-Me-benzyl connected with amide at C6 is essential for the binding affinity. The S-configured inhibitor (11j) displays 80 times more potency than the R-configure...

journal_title：Journal of computer-aided molecular design

authors： Chen Q,Cui W,Ji M

更新日期：2009-10-01 00:00:00

abstract：:The Drug Design Data Resource (D3R) Grand Challenges present an opportunity to assess, in the context of a blind predictive challenge, the accuracy and the limits of tools and methodologies designed to help guide pharmaceutical drug discovery projects. Here, we report the results of our participation in the D3R Grand ...

journal_title：Journal of computer-aided molecular design

authors： Sasmal S,El Khoury L,Mobley DL

更新日期：2020-02-01 00:00:00

abstract：:The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less acti...

journal_title：Journal of computer-aided molecular design

authors： Sanusi ZK,Govender T,Maguire GEM,Maseko SB,Lin J,Kruger HG,Honarparvar B

更新日期：2018-03-01 00:00:00

abstract：:In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters hig...

journal_title：Journal of computer-aided molecular design

authors： Nascimento ÉCM,Oliva M,Andrés J

更新日期：2018-05-01 00:00:00

abstract：:During the last few years, we have developed a docking protocol involving two steps: (i) the choice of the most appropriate docking software and parameters for the system of interest using structural and functional information available in public databases (PDB, ChEMBL, PubChem Assay, BindingDB, etc.); (ii) the dockin...

journal_title：Journal of computer-aided molecular design

authors： Chaput L,Selwa E,Elisée E,Iorga BI

更新日期：2019-01-01 00:00:00

abstract：:This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. Sampling can be tailored to a specific structural domain (e.g., peptides) by extracting torsional profiles from specific datasets and subsequently applying them to target mole...

journal_title：Journal of computer-aided molecular design

authors： Dorfman RJ,Smith KM,Masek BB,Clark RD

更新日期：2008-09-01 00:00:00

abstract：:Cheminformatics protocols have been developed and assessed that identify a small set of fragments which can represent the compounds in a chemical library for use in fragment-based ligand discovery. Six different methods have been implemented and tested on Input Libraries of compounds from three suppliers. The resultin...

journal_title：Journal of computer-aided molecular design

authors： Schulz MN,Landström J,Bright K,Hubbard RE

更新日期：2011-07-01 00:00:00

abstract：:Steric complementarity is a prerequisite for ligand-receptor recognition; this implies that drugs with a common receptor binding site should possess sterically similar binding surfaces. This principle is used as the basis for an automatic and unbiased method that superposes molecules. One molecule is rotated and trans...

journal_title：Journal of computer-aided molecular design

authors： Perkins TD,Mills JE,Dean PM

更新日期：1995-12-01 00:00:00

abstract：:In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screenin...

journal_title：Journal of computer-aided molecular design

authors： Nikitina N,Ivashko E,Tchernykh A

更新日期：2018-02-01 00:00:00

abstract：:As part of the fourth statistical assessment of modeling of proteins and ligands (sampl.eyesopen.com) prediction challenge, the strength of association of nine guests (1-9) binding to octa-acid host was determined by a combination of (1)H NMR and isothermal titration calorimetry. Association constants in sodium tetrab...

journal_title：Journal of computer-aided molecular design

authors： Gibb CL,Gibb BC

更新日期：2014-04-01 00:00:00

abstract：:The Epstein-Barr Nuclear Antigen 1 (EBNA1) is a critical protein encoded by the Epstein-Barr Virus (EBV). During latent infection, EBNA1 is essential for DNA replication and transcription initiation of viral and cellular genes and is necessary to immortalize primary B-lymphocytes. Nonetheless, the concept of EBNA1 as ...

journal_title：Journal of computer-aided molecular design

authors： Gianti E,Messick TE,Lieberman PM,Zauhar RJ

更新日期：2016-04-01 00:00:00

abstract：:The mounting evidences have shown that signal transducer and activator of transcription 3 (Stat3) is a critical target for cancer therapy. Recently, we developed a G-quartet oligonucleotide T40214 as a novel and potent Stat3 inhibitor. T40214 specifically inhibited DNA-binding activity of Stat3 and significantly suppr...

journal_title：Journal of computer-aided molecular design

authors： Zhu Q,Jing N

更新日期：2007-10-01 00:00:00

abstract：:The support vector machine, which is a novel algorithm from the machine learning community, was used to develop quantitation and classification models which can be used as a potential screening mechanism for a novel series of COX-2 selective inhibitors. Each compound was represented by calculated structural descriptor...

journal_title：Journal of computer-aided molecular design

authors： Liu HX,Zhang RS,Yao XJ,Liu MC,Hu ZD,Fan BT

更新日期：2004-06-01 00:00:00