Works matching IS 17582946 AND DT 2017 AND VI 9 AND IP 1

Results: 65

Consensus queries in ligand-based virtual screening experiments.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0248-5

By:

Berenger, Francois;
Vu, Oanh;
Meiler, Jens

Publication type:

Article

Computer-aided design of multi-target ligands at AR, AR and PDE10A, key proteins in neurodegenerative diseases.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0249-4

By:

Kalash, Leen;
Val, Cristina;
Azuaje, Jhonny;
Loza, María;
Svensson, Fredrik;
Zoufir, Azedine;
Mervin, Lewis;
Ladds, Graham;
Brea, José;
Glen, Robert;
Sotelo, Eddy;
Bender, Andreas

Publication type:

Article

Systematic exploration of multiple drug binding sites.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0255-6

By:

Bálint, Mónika;
Jeszenői, Norbert;
Horváth, István;
Spoel, David;
Hetényi, Csaba

Publication type:

Article

Can human experts predict solubility better than computers?

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0250-y

By:

Boobier, Samuel;
Osbourn, Anne;
Mitchell, John

Publication type:

Article

Scoria: a Python module for manipulating 3D molecular data.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0237-8

By:

Ropp, Patrick;
Friedman, Aaron;
Durrant, Jacob

Publication type:

Article

Efficient conformational ensemble generation of protein-bound peptides.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0246-7

By:

Yan, Yumeng;
Zhang, Di;
Huang, Sheng-You

Publication type:

Article

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0247-6

By:

Williams, Antony;
Grulke, Christopher;
Edwards, Jeff;
McEachran, Andrew;
Mansouri, Kamel;
Baker, Nancy;
Patlewicz, Grace;
Shah, Imran;
Wambaugh, John;
Judson, Richard;
Richard, Ann

Publication type:

Article

HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0254-7

By:

Feng, Ting;
Chen, Fu;
Kang, Yu;
Sun, Huiyong;
Liu, Hui;
Li, Dan;
Zhu, Feng;
Hou, Tingjun

Publication type:

Article

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0252-9

By:

Koch, Mathilde;
Duigou, Thomas;
Carbonell, Pablo;
Faulon, Jean-Loup

Publication type:

Article

BoBER: web interface to the base of bioisosterically exchangeable replacements.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0251-x

By:

Lešnik, Samo;
Škrlj, Blaž;
Eržen, Nika;
Bren, Urban;
Gobec, Stanislav;
Konc, Janez;
Janežič, Dušanka

Publication type:

Article

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0243-x

By:

Capoferri, Luigi;
van Dijk, Marc;
Rustenburg, Ariën;
Wassenaar, Tsjerk;
Kooi, Derk;
Rifai, Eko;
Vermeulen, Nico;
Geerke, Daan

Publication type:

Article

An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0244-9

By:

Su, Bo-Han;
Shen, Meng-Yu;
Harn, Yeu-Chern;
Wang, San-Yuan;
Schurz, Alioune;
Lin, Chieh;
Lin, Olivia;
Tseng, Yufeng

Publication type:

Article

A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0242-y

By:

Merkys, Andrius;
Mounet, Nicolas;
Cepellotti, Andrea;
Marzari, Nicola;
Gražulis, Saulius;
Pizzi, Giovanni

Publication type:

Article

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0241-z

By:

Hanwell, Marcus;
Jong, Wibe;
Harris, Christopher

Publication type:

Article

A review of parameters and heuristics for guiding metabolic pathfinding.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0239-6

By:

Kim, Sarah;
Peña, Matthew;
Moll, Mark;
Bennett, George;
Kavraki, Lydia

Publication type:

Article

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0240-0

By:

Tremouilhac, Pierre;
Nguyen, An;
Huang, Yu-Chieh;
Kotov, Serhii;
Lütjohann, Dominic;
Hübsch, Florian;
Jung, Nicole;
Bräse, Stefan

Publication type:

Article

Nonpher: computational method for design of hard-to-synthesize structures.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0206-2

By:

Voršilák, Milan;
Svozil, Daniel

Publication type:

Article

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Published in:: 2017
Publication type:: Correction Notice

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0203-5

By:

Sun, Jiangming;
Jeliazkova, Nina;
Chupakin, Vladimir;
Golib-Dzib, Jose-Felipe;
Engkvist, Ola;
Carlsson, Lars;
Wegner, Jörg;
Ceulemans, Hugo;
Georgiev, Ivan;
Jeliazkov, Vedrin;
Kochev, Nikolay;
Ashby, Thomas;
Chen, Hongming

Publication type:

Article

Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0200-8

By:

Takeda, Takako;
Hao, Ming;
Cheng, Tiejun;
Bryant, Stephen;
Wang, Yanli

Publication type:

Article

Large-scale virtual screening on public cloud resources with Apache Spark.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0204-4

By:

Capuccini, Marco;
Ahmed, Laeeq;
Schaal, Wesley;
Laure, Erwin;
Spjuth, Ola

Publication type:

Article

G.A.M.E.: GPU-accelerated mixture elucidator.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0238-7

By:

Schurz, Alioune;
Su, Bo-Han;
Tu, Yi-Shu;
Lu, Tony;
Lin, Olivia;
Tseng, Yufeng

Publication type:

Article

Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0236-9

By:

Polanski, Jaroslaw;
Tkocz, Aleksandra;
Kucia, Urszula

Publication type:

Article

Molecular de-novo design through deep reinforcement learning.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0235-x

By:

Olivecrona, Marcus;
Blaschke, Thomas;
Engkvist, Ola;
Chen, Hongming

Publication type:

Article

Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0233-z

By:

An, Ji-Yong;
Zhang, Lei;
Zhou, Yong;
Zhao, Yu-Jun;
Wang, Da-Fu

Publication type:

Article

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0234-y

By:

Skinnider, Michael;
Dejong, Chris;
Franczak, Brian;
McNicholas, Paul;
Magarvey, Nathan

Publication type:

Article

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0232-0

By:

Lenselink, Eelke;
Dijke, Niels;
Bongers, Brandon;
Papadatos, George;
Vlijmen, Herman;
Kowalczyk, Wojtek;
IJzerman, Adriaan;
Westen, Gerard

Publication type:

Article

Efficiency of different measures for defining the applicability domain of classification models.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0230-2

By:

Klingspohn, Waldemar;
Mathea, Miriam;
Laak, Antonius;
Heinrich, Nikolaus;
Baumann, Knut

Publication type:

Article

Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0229-8

By:

Narayanan, Dilip;
Gani, Osman;
Gruber, Franz;
Engh, Richard

Publication type:

Article

Adverse drug reactions triggered by the common HLA-B*57:01 variant: a molecular docking study.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0202-6

By:

Driessche, George;
Fourches, Denis

Publication type:

Article

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0226-y

By:

Koutsoukas, Alexios;
Monaghan, Keith;
Li, Xiaoli;
Huan, Jun

Publication type:

Article

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0223-1

By:

Preciat Gonzalez, German;
El Assal, Lemmer;
Noronha, Alberto;
Thiele, Ines;
Haraldsdóttir, Hulda;
Fleming, Ronan

Publication type:

Article

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0228-9

By:

Lee, Man-Ling;
Aliagas, Ignacio;
Feng, Jianwen;
Gabriel, Thomas;
O'Donnell, T.;
Sellers, Benjamin;
Wiswedel, Bernd;
Gobbi, Alberto

Publication type:

Article

Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0227-x

By:

Chaput, Ludovic;
Mouawad, Liliane

Publication type:

Article

An algorithm to identify functional groups in organic molecules.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0225-z

By:

Ertl, Peter

Publication type:

Article

QuBiLS- MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0211-5

By:

Valdés-Martiní, José;
Marrero-Ponce, Yovani;
García-Jacas, César;
Martinez-Mayorga, Karina;
Barigye, Stephen;
Vaz d'Almeida, Yasser;
Pham-The, Hai;
Pérez-Giménez, Facundo;
Morell, Carlos

Publication type:

Article

RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0224-0

By:

Kaspi, Omer;
Yosipof, Abraham;
Senderowitz, Hanoch

Publication type:

Article

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0220-4

By:

Willighagen, Egon;
Mayfield, John;
Alvarsson, Jonathan;
Berg, Arvid;
Carlsson, Lars;
Jeliazkova, Nina;
Kuhn, Stefan;
Pluskal, Tomáš;
Rojas-Chertó, Miquel;
Spjuth, Ola;
Torrance, Gilleain;
Evelo, Chris;
Guha, Rajarshi;
Steinbeck, Christoph

Publication type:

Article

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0219-x

By:

Blaženović, Ivana;
Kind, Tobias;
Torbašinović, Hrvoje;
Obrenović, Slobodan;
Mehta, Sajjan;
Tsugawa, Hiroshi;
Wermuth, Tobias;
Schauer, Nicolas;
Jahn, Martina;
Biedendieck, Rebekka;
Jahn, Dieter;
Fiehn, Oliver

Publication type:

Article

Electronic lab notebooks: can they replace paper?

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0221-3

By:

Kanza, Samantha;
Willoughby, Cerys;
Gibbins, Nicholas;
Whitby, Richard;
Frey, Jeremy;
Erjavec, Jana;
Zupančič, Klemen;
Hren, Matjaž;
Kovač, Katarina

Publication type:

Article

CPANNatNIC software for counter-propagation neural network to assist in read-across.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0218-y

By:

Drgan, Viktor;
Župerl, Špela;
Vračko, Marjan;
Cappelli, Claudia;
Novič, Marjana

Publication type:

Article

Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0216-0

By:

Gürsoy, Oya;
Smieško, Martin

Publication type:

Article

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0213-3

By:

Schäfer, Till;
Kriege, Nils;
Humbeck, Lina;
Klein, Karsten;
Koch, Oliver;
Mutzel, Petra

Publication type:

Article

ChemSAR: an online pipelining platform for molecular SAR modeling.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0215-1

By:

Dong, Jie;
Yao, Zhi-Jiang;
Zhu, Min-Feng;
Wang, Ning-Ning;
Lu, Ben;
Chen, Alex;
Lu, Ai-Ping;
Miao, Hongyu;
Zeng, Wen-Bin;
Cao, Dong-Sheng

Publication type:

Article

Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0214-2

By:

Senger, Stefan

Publication type:

Article

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0212-4

By:

Shang, Jun;
Sun, Huiyong;
Liu, Hui;
Chen, Fu;
Tian, Sheng;
Pan, Peichen;
Li, Dan;
Kong, Dexin;
Hou, Tingjun

Publication type:

Article

SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0209-z

By:

He, Tong;
Heidemeyer, Marten;
Ban, Fuqiang;
Cherkasov, Artem;
Ester, Martin

Publication type:

Article

A possible extension to the RInChI as a means of providing machine readable process data.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0210-6

By:

Jacob, Philipp-Maximilian;
Lan, Tian;
Goodman, Jonathan;
Lapkin, Alexei

Publication type:

Article

Critical Assessment of Small Molecule Identification 2016: automated methods.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0207-1

By:

Schymanski, Emma;
Ruttkies, Christoph;
Krauss, Martin;
Brouard, Céline;
Kind, Tobias;
Dührkop, Kai;
Allen, Felicity;
Vaniya, Arpana;
Verdegem, Dries;
Böcker, Sebastian;
Rousu, Juho;
Shen, Huibin;
Tsugawa, Hiroshi;
Sajed, Tanvir;
Fiehn, Oliver;
Ghesquière, Bart;
Neumann, Steffen

Publication type:

Article

The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0208-0

By:

Kim, Hyoungrae;
Jang, Cheongyun;
Yadav, Dharmendra;
Kim, Mi-hyun

Publication type:

Article