BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.

abstract：:Interfacial hydration strongly influences interactions between biomolecules. For example, drug-target complexes are often stabilized by hydration networks formed between hydrophilic residues and water molecules at the interface. Exhaustive exploration of hydration networks is challenging for experimental as well as th...

journal_title：Journal of chemical information and modeling

authors： Jeszenői N,Bálint M,Horváth I,van der Spoel D,Hetényi C

更新日期：2016-01-25 00:00:00

abstract：:A giant technological leap in the field of cryo-electron microscopy (cryo-EM) has assured the achievement of near-atomic resolution structures of biological macromolecules. As a recognition of this accomplishment, the Nobel Prize in Chemistry was awarded in 2017 to Jacques Dubochet, Joachim Frank, and Richard Henderso...

journal_title：Journal of chemical information and modeling

authors： Akbar S,Mozumder S,Sengupta J

更新日期：2020-05-26 00:00:00

abstract：:Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Curren...

journal_title：Journal of chemical information and modeling

authors： Ashtawy HM,Mahapatra NR

更新日期：2018-01-22 00:00:00

abstract：:Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations ar...

journal_title：Journal of chemical information and modeling

authors： Moghadam BT,Alvarsson J,Holm M,Eklund M,Carlsson L,Spjuth O

更新日期：2015-01-26 00:00:00

abstract：:Whereas 400 million distinct compounds are now purchasable within the span of a few weeks, the biological activities of most are unknown. To facilitate access to new chemistry for biology, we have combined the Similarity Ensemble Approach (SEA) with the maximum Tanimoto similarity to the nearest bioactive to predict a...

journal_title：Journal of chemical information and modeling

authors： Irwin JJ,Gaskins G,Sterling T,Mysinger MM,Keiser MJ

更新日期：2018-01-22 00:00:00

abstract：:Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spect...

journal_title：Journal of chemical information and modeling

authors： Cortes-Ciriano I,Bender A

更新日期：2015-12-28 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：:Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguis...

journal_title：Journal of chemical information and modeling

authors： Guterres H,Im W

更新日期：2020-04-27 00:00:00

abstract：:It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builde...

journal_title：Journal of chemical information and modeling

authors： Fechner U,Schneider G

更新日期：2006-03-01 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：:We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published cryst...

journal_title：Journal of chemical information and modeling

authors： Sai Ram KV,Rambabu G,Sarma JA,Desiraju GR

更新日期：2006-07-01 00:00:00

abstract：:Several drugs elicit their therapeutic efficacy by modulating multiple cellular targets and possess varied polypharmacological actions. The identification of the molecular targets of a potent bioactive molecule is essential in determining its overall polypharmacological profile. Experimental procedures are expensive a...

journal_title：Journal of chemical information and modeling

authors： Dutta D,Das R,Mandal C,Mandal C

更新日期：2018-01-22 00:00:00

abstract：:The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can p...

journal_title：Journal of chemical information and modeling

authors： Vincent MA,Hillier IH

更新日期：2014-08-25 00:00:00

abstract：:Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. The PythoMS framewor...

journal_title：Journal of chemical information and modeling

authors： Yunker LPE,Donnecke S,Ting M,Yeung D,McIndoe JS

更新日期：2019-04-22 00:00:00

abstract：:We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automate...

journal_title：Journal of chemical information and modeling

authors： Makeneni S,Foley BL,Woods RJ

更新日期：2014-10-27 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：:Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description...

journal_title：Journal of chemical information and modeling

authors： Barrera MC,Jorge M

更新日期：2020-03-23 00:00:00

abstract：:The Common Instrument Middleware Architecture (CIMA) aims at Grid-enabling a wide range of scientific instruments and sensors to enable easy access to and sharing and storage of data produced by these instruments and sensors. This paper describes the implementation of CIMA applied to the field of single-crystal X-ray ...

journal_title：Journal of chemical information and modeling

authors： Bramley R,Chiu K,Devadithya T,Gupta N,Hart C,Huffman JC,Huffman K,Ma Y,McMullen DF

更新日期：2006-05-01 00:00:00

abstract：:Reversible and irreversible covalent ligands are advanced cysteine protease inhibitors in the drug development pipeline. K777 is an irreversible inhibitor of cruzain, a necessary enzyme for the survival of the Trypanosoma cruzi (T. cruzi) parasite, the causative agent of Chagas disease. Despite their importance, irrev...

journal_title：Journal of chemical information and modeling

authors： Silva JRA,Cianni L,Araujo D,Batista PHJ,de Vita D,Rosini F,Leitão A,Lameira J,Montanari CA

更新日期：2020-03-23 00:00:00

abstract：:Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical e...

journal_title：Journal of chemical information and modeling

authors： Bisignano P,Lambruschini C,Bicego M,Murino V,Favia AD,Cavalli A

更新日期：2012-12-21 00:00:00

abstract：:Activity cliffs are formed by structurally similar compounds having large potency differences. Coordinated activity cliffs evolve when compounds within groups of structural neighbors form multiple cliffs with different partners, giving rise to local networks of cliffs in a data set. Using particle swarm optimization, ...

journal_title：Journal of chemical information and modeling

authors： Namasivayam V,Bajorath J

更新日期：2012-04-23 00:00:00

abstract：:The emergence of a large amount of pharmacological, genomic, and network knowledge data provides new challenges and opportunities for drug discovery and development. Identification of real small-molecule drug (SM)-miRNA associations is not only important in the development of effective drug repositioning but also cruc...

journal_title：Journal of chemical information and modeling

authors： Shen C,Luo J,Lai Z,Ding P

更新日期：2020-08-24 00:00:00

abstract：:Naturally occurring anticancer compounds represent about half of the chemotherapeutic drugs which have been put in the market against cancer until date. Computer-based or in silico virtual screening methods are often used in lead/hit discovery protocols. In this study, the "drug-likeness" of ~400 compounds from Africa...

journal_title：Journal of chemical information and modeling

authors： Ntie-Kang F,Nwodo JN,Ibezim A,Simoben CV,Karaman B,Ngwa VF,Sippl W,Adikwu MU,Mbaze LM

更新日期：2014-09-22 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：: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：:A novel pharmacophore descriptor Flexophore is presented, which considers molecular flexibility when comparing descriptor similarities. The descriptor is a complete reduced graph of the underlying molecule. Its nodes are represented by enhanced MM2 atom types, while the edge descriptions encode the molecular flexibili...

journal_title：Journal of chemical information and modeling

authors： von Korff M,Freyss J,Sander T

更新日期：2008-04-01 00:00:00

abstract：:Our main objective was to compile a data set of high-quality protein-fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How t...

journal_title：Journal of chemical information and modeling

authors： Favia AD,Bottegoni G,Nobeli I,Bisignano P,Cavalli A

更新日期：2011-11-28 00:00:00

abstract：:Deep learning has drawn significant attention in different areas including drug discovery. It has been proposed that it could outperform other machine learning algorithms, especially with big data sets. In the field of pharmaceutical industry, machine learning models are built to understand quantitative structure-acti...

journal_title：Journal of chemical information and modeling

authors： Zhou Y,Cahya S,Combs SA,Nicolaou CA,Wang J,Desai PV,Shen J

更新日期：2019-03-25 00:00:00

abstract：:Solute-solvent interactions are critical for biomolecular stability and recognition. Explicit solvent molecular dynamics (MD) simulations are routinely used to probe such interactions. However, detailed analyses and interpretation of the hydration patterns seen in MD simulations can be both complex and time-consuming....

journal_title：Journal of chemical information and modeling

authors： Pradhan MR,Nguyen MN,Kannan S,Fox SJ,Kwoh CK,Lane DP,Verma CS

更新日期：2019-07-22 00:00:00