Benchmark data set for in silico prediction of Ames mutagenicity.

abstract：:The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBb...

journal_title：Journal of chemical information and modeling

authors： Li Y,Yang J

更新日期：2017-04-24 00:00:00

abstract：:Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissu...

journal_title：Journal of chemical information and modeling

authors： Salum LB,Polikarpov I,Andricopulo AD

更新日期：2008-11-01 00:00:00

abstract：:Great attention has been paid to the clinical significance of phosphodiesterase 5 (PDE5) inhibitors, such as sildenafil, tadalafil, and vardenafil widely used for erectile dysfunction. However, sildenafil causes side effects on visual functions since it shows similar potencies to inhibit PDE5 and PDE6, whereas tadalaf...

journal_title：Journal of chemical information and modeling

authors： Huang YY,Li Z,Cai YH,Feng LJ,Wu Y,Li X,Luo HB

更新日期：2013-11-25 00:00:00

abstract：:Side-chain modeling is critical for protein structure prediction since the uniqueness of the protein structure is largely determined by its side-chain packing conformation. In this paper, differing from most approaches that rely on rotamer library sampling, we first propose a novel side-chain rotamer prediction method...

journal_title：Journal of chemical information and modeling

authors： Xu G,Wang Q,Ma J

更新日期：2020-12-28 00:00:00

abstract：:Virtual screening (VS) can be accomplished in either ligand- or structure-based methods. In recent times, an increasing number of 2D fingerprint and 3D shape similarity methods have been used in ligand-based VS. To evaluate the performance of these ligand-based methods, retrospective VS was performed on a tailored dir...

journal_title：Journal of chemical information and modeling

authors： Hu G,Kuang G,Xiao W,Li W,Liu G,Tang Y

更新日期：2012-05-25 00:00:00

abstract：:SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provi...

journal_title：Journal of chemical information and modeling

authors： Schwartz J,Awale M,Reymond JL

更新日期：2013-08-26 00:00:00

abstract：:As a result of the widespread industrial use of polychlorinated hydrocarbons, they have accumulated in nearly all types of environmental compartments, especially in aquatic systems. Particularly, chloroaromatics are among the most undesirable industrial effluents because of their persistence and toxicity. To predict c...

journal_title：Journal of chemical information and modeling

authors： Ivanciuc T,Ivanciuc O,Klein DJ

更新日期：2005-07-01 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：:Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

journal_title：Journal of chemical information and modeling

authors： Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

更新日期：2020-12-28 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：: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：:An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are...

journal_title：Journal of chemical information and modeling

authors： Ibrahim P,Wifling D,Clark T

更新日期：2019-09-23 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：: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：: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：:Curvularia lunata is a dark pigmented fungus that is the causative agent of several diseases in plants and in both immunodeficient and immunocompetent patients. 1,8-Dihydroxynaphthalene-melanin is found in the cell wall of C. lunata and is believed to be the important virulence factor of dematiaceous fungi. Trihydroxy...

journal_title：Journal of chemical information and modeling

authors： Brunskole Svegelj M,Turk S,Brus B,Lanisnik Rizner T,Stojan J,Gobec S

更新日期：2011-07-25 00:00:00

abstract：:Ab initio quantum-chemistry programs produce and use large amounts of data, which are usually stored on disk in the form of binary files. A FORTRAN library, named Q5Cost, has been designed and implemented in order to allow the storage of these data sets in a special data format built with the HDF5 technology. This dat...

journal_title：Journal of chemical information and modeling

authors： Borini S,Monari A,Rossi E,Tajti A,Angeli C,Bendazzoli GL,Cimiraglia R,Emerson A,Evangelisti S,Maynau D,Sanchez-Marin J,Szalay PG

更新日期：2007-05-01 00:00:00

abstract：:In the present contribution, we have developed a database, called the FAR-database, where the acronym FAR stands for Fused Aromatic Rings, which presents the results of nuclear independent chemical shifts calculations, NICS(0), NICS(1), NICS(0)ZZ, and NICS(1)ZZ, of 660 neutral benzenoid-PAHs and cyclopenta-fused PAHs....

journal_title：Journal of chemical information and modeling

authors： Alvarez-Ramírez F,Ruiz-Morales Y

更新日期：2020-02-24 00:00:00

abstract：:Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...

journal_title：Journal of chemical information and modeling

authors： Galat A

更新日期：2015-09-28 00:00:00

abstract：:Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. Gabapentin and pregabalin are some of the most successful drugs in the treatment of epilepsy and n...

journal_title：Journal of chemical information and modeling

authors： Kotev M,Pascual R,Almansa C,Guallar V,Soliva R

更新日期：2018-08-27 00:00:00

abstract：:Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many pro...

journal_title：Journal of chemical information and modeling

authors： Brown WM,Sasson A,Bellew DR,Hunsaker LA,Martin S,Leitao A,Deck LM,Vander Jagt DL,Oprea TI

更新日期：2008-08-01 00:00:00

abstract：:Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specifi...

journal_title：Journal of chemical information and modeling

authors： Gaudreault F,Najmanovich RJ

更新日期：2015-07-27 00:00:00

abstract：:The large volume of protein-ligand structures now available enables innovative and efficient protocols in computational FBDD (Fragment-Based Drug Design) to be proposed based on experimental data. In this work, we build a database of MED-Portions, where a MED-Portion is a new structural object encoding protein-fragmen...

journal_title：Journal of chemical information and modeling

authors： Moriaud F,Doppelt-Azeroual O,Martin L,Oguievetskaia K,Koch K,Vorotyntsev A,Adcock SA,Delfaud F

更新日期：2009-02-01 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：:Over the last few decades, anticancer peptides (ACPs) have turned into potential warheads against cancer. Apart from small molecules and monoclonal antibodies, ACPs have been proven to be effective against cancer cells. ACPs are small cationic peptides that selectively bind to the negatively charged cancer cell membra...

journal_title：Journal of chemical information and modeling

authors： Singh M,Kumar V,Sikka K,Thakur R,Harioudh MK,Mishra DP,Ghosh JK,Siddiqi MI

更新日期：2020-01-27 00:00:00

abstract：:To promote more productive combinatorial endeavors, the Diversity Space methodology introduced here enables similarity comparisons at the library level. Particularly at an early screening stage, when little or no information is available regarding the pharmacophoric entities necessary for binding, it is more efficient...

journal_title：Journal of chemical information and modeling

authors： Fitzgerald SH,Sabat M,Geysen HM

更新日期：2006-07-01 00:00:00

abstract：:Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TRalpha and TRbeta. Several pharmacological effects mediated by TRbeta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TRbeta activation may el...

journal_title：Journal of chemical information and modeling

authors： Valadares NF,Salum LB,Polikarpov I,Andricopulo AD,Garratt RC

更新日期：2009-11-01 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：:Machine learning has exhibited powerful capabilities in many areas. However, machine learning models are mostly database dependent, requiring a new model if the database changes. Therefore, a universal model is highly desired to accommodate the widest variety of databases. Fortunately, this universality may be achieve...

journal_title：Journal of chemical information and modeling

authors： Li W,Miao W,Cui J,Fang C,Su S,Li H,Hu L,Lu Y,Chen G

更新日期：2019-05-28 00:00:00

abstract：:To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

journal_title：Journal of chemical information and modeling

authors： Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

更新日期：2009-05-01 00:00:00