Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

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：:One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of...

journal_title：Journal of chemical information and modeling

authors： da Costa CHS,Bonatto V,Dos Santos AM,Lameira J,Leitão A,Montanari CA

更新日期：2020-02-24 00:00:00

abstract：:Given the essential role played by protein kinases in regulating cellular pathways, their dysregulation can result in the onset and/or progression of various human diseases. Structural analysis of diverse protein kinases suggests that these proteins exhibit a remarkable plasticity that allows them to adopt distinct co...

journal_title：Journal of chemical information and modeling

authors： Gomez-Gutierrez P,Rubio-Martinez J,Perez JJ

更新日期：2017-10-23 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：:Iterative screening has emerged as a promising approach to increase the efficiency of high-throughput screening (HTS) campaigns in drug discovery. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models. One of the challenges of iterative screenin...

journal_title：Journal of chemical information and modeling

authors： Buendia R,Kogej T,Engkvist O,Carlsson L,Linusson H,Johansson U,Toccaceli P,Ahlberg E

更新日期：2019-03-25 00:00:00

abstract：:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...

journal_title：Journal of chemical information and modeling

authors： ten Brink T,Exner TE

更新日期：2009-06-01 00:00:00

abstract：:Porcupine is a component of the Wnt pathway which regulates cell proliferation, migration, stem cell self-renewal, and differentiation. The Wnt pathway has been shown to be dysregulated in a variety of cancers. Porcupine is a membrane bound O-acyltransferase that palmitoylates Wnt. Inhibiting porcupine blocks the secr...

journal_title：Journal of chemical information and modeling

authors： Poulsen A,Ho SY,Wang W,Alam J,Jeyaraj DA,Ang SH,Tan ES,Lin GR,Cheong VW,Ke Z,Lee MA,Keller TH

更新日期：2015-07-27 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：:Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, w...

journal_title：Journal of chemical information and modeling

authors： White AD,Keefe AJ,Nowinski AK,Shao Q,Caldwell K,Jiang S

更新日期：2013-02-25 00:00:00

abstract：:The human androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of prostate cancer (PCa). Many forms of castration-resistant prostate cancer (CRPC) still rely on the AR for survival. Currently used antiandrogens face clinical limitations as drug ...

journal_title：Journal of chemical information and modeling

authors： Paul N,Carabet LA,Lallous N,Yamazaki T,Gleave ME,Rennie PS,Cherkasov A

更新日期：2016-12-27 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：:LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallogra...

journal_title：Journal of chemical information and modeling

authors： Wan H,Chang S,Hu JP,Tian YX,Tian XH

更新日期：2015-04-27 00:00:00

abstract：:Universal generative topographic maps (GTMs) provide two-dimensional representations of chemical space selected for their "polypharmacological competence", that is, the ability to simultaneously represent meaningful activity and property landscapes, associated with many distinct targets and properties. Several such GT...

journal_title：Journal of chemical information and modeling

authors： Casciuc I,Zabolotna Y,Horvath D,Marcou G,Bajorath J,Varnek A

更新日期：2019-01-28 00:00:00

abstract：:Many of the conventional similarity methods assume that molecular fragments that do not relate to biological activity carry the same weight as the important ones. One possible approach to this problem is to use the Bayesian inference network (BIN), which models molecules and reference structures as probabilistic infer...

journal_title：Journal of chemical information and modeling

authors： Abdo A,Salim N

更新日期：2011-01-24 00:00:00

abstract：:Telomere maintenance is a universal cancer hallmark, and small molecules that disrupt telomere maintenance generally have anticancer properties. Since the vast majority of cancer cells utilize telomerase activity for telomere maintenance, the enzyme has been considered as an anticancer drug target. Recently, rational ...

journal_title：Journal of chemical information and modeling

authors： Shirgahi Talari F,Bagherzadeh K,Golestanian S,Jarstfer M,Amanlou M

更新日期：2015-12-28 00:00:00

abstract：:Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms ...

journal_title：Journal of chemical information and modeling

authors： Carl N,Konc J,Vehar B,Janezic D

更新日期：2010-10-25 00:00:00

abstract：:Knowledge of the interactions between drugs and transporters is important for drug discovery and development as well as for the evaluation of their clinical safety. We recently developed a text-mining system for the automatic extraction of information on chemical-CYP3A4 interactions from the literature. This system is...

journal_title：Journal of chemical information and modeling

authors： Yoshida S,Yamashita F,Ose A,Maeda K,Sugiyama Y,Hashida M

更新日期：2013-10-28 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

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：: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：: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 configuring of a radial basis function network (RBFN) consists of selecting the network parameters (centers and widths in RBF units and weights between the hidden and output layers) and network architecture. The issues of suboptimum and overfitting, however, often occur in RBFN configuring. This paper presented a ...

journal_title：Journal of chemical information and modeling

authors： Zhou YP,Jiang JH,Lin WQ,Zou HY,Wu HL,Shen GL,Yu RQ

更新日期：2006-11-01 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：:Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public database...

journal_title：Journal of chemical information and modeling

authors： Pan Y,Cheng T,Wang Y,Bryant SH

更新日期：2014-02-24 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：: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：:The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...

journal_title：Journal of chemical information and modeling

authors： Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

更新日期：2014-02-24 00:00:00

abstract：:We implemented a fragment-based de novo design algorithm for a population-based optimization of molecular structures. The concept is grounded on an evolution strategy with mutation and crossover operators for structure breeding. Molecular building blocks were obtained from the pseudo-retrosynthesis of a collection of ...

journal_title：Journal of chemical information and modeling

authors： Fechner U,Schneider G

更新日期：2007-03-01 00:00:00

abstract：:Histone deacetylases (HDACs) are an important class of drug targets for the treatment of cancers, neurodegenerative diseases, and other types of diseases. Virtual screening (VS) has become fairly effective approaches for drug discovery of novel and highly selective histone deacetylase inhibitors (HDACIs). To facilitat...

journal_title：Journal of chemical information and modeling

authors： Xia J,Tilahun EL,Kebede EH,Reid TE,Zhang L,Wang XS

更新日期：2015-02-23 00:00:00

abstract：:Protein farnesyltransferase (FTase) is an important anticancer drug target. In an effort to develop isoprenoid diphosphate-based FTase inhibitors, striking variations have been observed in the ability of conservatively modified analogues to bind to the enzyme. For example, 2Z-GGPP is an alternative substrate with high...

journal_title：Journal of chemical information and modeling

authors： Henriksen BS,Zahn TJ,Evanseck JD,Firestine SM,Gibbs RA

更新日期：2005-07-01 00:00:00