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ORCIDJournal of Cheminformatics, Volume 9
Volume 9, Number 1, December 2017
- Masataka Kuroda
:
A novel descriptor based on atom-pair properties. 1:1-1:11 - Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-Yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo, Hwangseo Park:
NPCARE: database of natural products and fractional extracts for cancer regulation. 2:1-2:9 - Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N. Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo, Emanuele Amata:
S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands. 3:1-3:9 - Matthew J. Harvey, Andrew McLean, Henry S. Rzepa:
A metadata-driven approach to data repository design. 4:1-4:10 - Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin, Chun-Wei Tung:
SkinSensDB: a curated database for skin sensitization assays. 5:1-5:6 - Sandip De, Felix Musil, Teresa Ingram, Carsten Baldauf, Michele Ceriotti:
Mapping and classifying molecules from a high-throughput structural database. 6:1-6:14 - Julio Cesar Dias Lopes, Fábio Mendes dos Santos, Andrelly Martins-José, Koen Augustyns, Hans De Winter:
The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability. 7:1-7:11 - Marcus Johansson, Valera Veryazov:
Automatic procedure for generating symmetry adapted wavefunctions. 8:1-8:8 - Eli Fernández-de Gortari, César R. García-Jacas, Karina Martínez-Mayorga, José L. Medina-Franco:
Database fingerprint (DFP): an approach to represent molecular databases. 9:1-9:9 - John W. Mayfield, Roger A. Sayle:
Technical implications of new IUPAC elements in cheminformatics. 10:1-10:3 - Mahendra Awale, Jean-Louis Reymond:
The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. 11:1-11:10 - Martin Loos, Heinz Singer:
Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data. 12:1-12:11 - George van den Driessche, Denis Fourches:
Adverse drug reactions triggered by the common HLA-B*57: 01 variant: a molecular docking study. 13:1-13:17 - Mark I. Borkum, Patrick Reardon, Ronald C. Taylor, Nancy G. Isern:
Modeling framework for isotopic labeling of heteronuclear moieties. 14:1-14:11 - Marco Capuccini, Laeeq Ahmed, Wesley Schaal, Erwin Laure, Ola Spjuth:
Large-scale virtual screening on public cloud resources with Apache Spark. 15:1-15:6 - Takako Takeda, Ming Hao, Tiejun Cheng, Stephen H. Bryant, Yanli Wang:
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. 16:1-16:9 - Jiangming Sun, Nina Jeliazkova, Vladimir I. Chupakhin, José Felipe Golib Dzib, Ola Engkvist, Lars Carlsson, Jörg K. Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay T. Kochev, Thomas J. Ashby, Hongming Chen:
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. 17:1-17:9 - Steve O'Hagan, Douglas B. Kell:
Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. 18:1-18:17 - Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita, Masanori Arita:
Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. 19:1-19:12 - Milan Vorsilák, Daniel Svozil:
Nonpher: computational method for design of hard-to-synthesize structures. 20:1-20:7 - Hyoungrae Kim, Cheongyun Jang, Dharmendra Kumar Yadav, Mi-Hyun Kim:
The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix. 21:1-21:26 - Emma Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen, Hiroshi Tsugawa, Tanvir Sajed, Oliver Fiehn, Bart Ghesquière, Steffen Neumann:
Critical Assessment of Small Molecule Identification 2016: automated methods. 22:1-22:21 - Philipp-Maximilian Jacob, Tian Lan, Jonathan M. Goodman, Alexei A. Lapkin:
A possible extension to the RInChI as a means of providing machine readable process data. 23:1-23:12 - Tong He, Marten Heidemeyer, Fuqiang Ban, Artem Cherkasov, Martin Ester:
SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines. 24:1-24:14 - Jun Shang, Huiyong Sun, Hui Liu, Fu Chen, Sheng Tian, Peichen Pan, Dan Li, De-Xin Kong, Tingjun Hou:
Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. 25:1-25:16 - Stefan Senger:
Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses. 26:1-26:8 - Jie Dong, Zhi-Jiang Yao, Min-Feng Zhu, Ning-Ning Wang, Ben Lu, Alex F. Chen, Aiping Lu, Hongyu Miao, Wen-Bin Zeng, Dong-Sheng Cao:
ChemSAR: an online pipelining platform for molecular SAR modeling. 27:1-27:13 - Till Schäfer, Nils M. Kriege, Lina Humbeck, Karsten Klein, Oliver Koch, Petra Mutzel:
Scaffold Hunter: a comprehensive visual analytics framework for drug discovery. 28:1-28:18 - Oya Gürsoy, Martin Smiesko:
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we? 29:1-29:13 - Viktor Drgan, Spela Zuperl, Marjan Vracko, Claudia Cappelli, Marjana Novic:
CPANNatNIC software for counter-propagation neural network to assist in read-across. 30:1-30:15 - Samantha Kanza, Cerys Willoughby, Nicholas Gibbins, Richard J. Whitby, Jeremy G. Frey, Jana Erjavec, Klemen Zupancic, Matjaz Hren, Katarina Kovac:
Electronic lab notebooks: can they replace paper? 31:1-31:15 - Ivana Blazenovic, Tobias Kind, Hrvoje Torbasinovic, Slobodan Obrenovic, Sajjan S. Mehta, Hiroshi Tsugawa, Tobias Wermuth, Nicolas Schauer, Martina Jahn, Rebekka Biedendieck, Dieter Jahn, Oliver Fiehn:
Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. 32:1-32:12 - Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck:
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. 33:1-33:19 - Omer Kaspi, Abraham Yosipof, Hanoch Senderowitz:
RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells. 34:1-34:15 - José R. Valdés-Martiní, Yovani Marrero-Ponce, César R. García-Jacas, Karina Martínez-Mayorga, Stephen J. Barigye, Yasser Silveira Vaz d'Almeida, Hai Pham-The, Facundo Pérez-Giménez, Carlos A. Morell:
QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations. 35:1-35:26 - Peter Ertl:
An algorithm to identify functional groups in organic molecules. 36:1-36:7 - Ludovic Chaput, Liliane Mouawad:
Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds. 37:1-37:18 - Man-Ling Lee, Ignacio Aliagas, Jianwen A. Feng, Thomas R. Gabriel, T. J. O'Donnell, Benjamin D. Sellers, Bernd Wiswedel, Alberto Gobbi:
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery. 38:1-38:14 - German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming:
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. 39:1-39:15 - Rajarshi Guha, Egon L. Willighagen:
Helping to improve the practice of cheminformatics. 40:1-40:2 - Jiangming Sun, Nina Jeliazkova, Vladimir I. Chupakhin, José Felipe Golib Dzib, Ola Engkvist, Lars Carlsson, Jörg K. Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay T. Kochev, Thomas J. Ashby, Hongming Chen:
Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. 41:1 - Alexios Koutsoukas, Keith J. Monaghan, Xiaoli Li, Jun Huan:
Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data. 42:1-42:13 - Dilip Narayanan, Osman A. B. S. M. Gani, Franz X. E. Gruber, Richard A. Engh:
Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR. 43:1-43:19 - Marcus Olivecrona, Thomas Blaschke, Ola Engkvist, Hongming Chen:
Molecular de-novo design through deep reinforcement learning. 48:1-48:14 - Marcus D. Hanwell, Wibe A. de Jong, Christopher J. Harris:
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application. 55:1-55:10 - Andrius Merkys, Nicolas Mounet, Andrea Cepellotti, Nicola Marzari, Saulius Grazulis, Giovanni Pizzi:
A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD. 56:1-56:11 - Bo-Han Su, Meng-yu Shen, Yeu-Chern Harn, San-Yuan Wang, Alioune Schurz, Chieh Lin, Olivia A. Lin, Yufeng J. Tseng:
An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm. 57:1-57:15 - Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko Aditya Rifai, Nico P. E. Vermeulen, Daan P. Geerke:
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. 58:1-58:13 - Yumeng Yan, Di Zhang, Sheng-You Huang:
Efficient conformational ensemble generation of protein-bound peptides. 59:1-59:13 - Francois Berenger, Oanh Vu, Jens Meiler:
Consensus queries in ligand-based virtual screening experiments. 60:1-60:13 - Antony J. Williams, Christopher M. Grulke, Jeff Edwards, Andrew D. McEachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, Imran Shah, John Wambaugh, Richard S. Judson, Ann M. Richard:
The CompTox Chemistry Dashboard: a community data resource for environmental chemistry. 61:1-61:27 - Samo Lesnik, Blaz Skrlj, Nika Erzen, Urban Bren, Stanislav Gobec, Janez Konc, Dusanka Janezic:
BoBER: web interface to the base of bioisosterically exchangeable replacements. 62:1-62:8 - Samuel Boobier, Anne Osbourn, John B. O. Mitchell:
Can human experts predict solubility better than computers? 63:1-63:14 - Mathilde Koch, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon:
Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. 64:1-64:17 - Mónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi:
Systematic exploration of multiple drug binding sites. 65:1-65:12 - Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou:
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. 66:1-66:15 - Leen Kalash, Cristina Val, Jhonny Azuaje, Maria Isabel Loza, Fredrik Svensson, Azedine Zoufir, Lewis H. Mervin, Graham Ladds, José M. Brea, Robert C. Glen, Eddy Sotelo, Andreas Bender:
Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. 67:1-67:19 - Waldemar Klingspohn, Miriam Mathea, Antonius ter Laak, Nikolaus Heinrich, Knut Baumann:
Efficiency of different measures for defining the applicability domain of classification models. 44 - Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen:
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. 45 - Michael A. Skinnider, Chris A. Dejong, Brian C. Franczak, Paul D. McNicholas, Nathan A. Magarvey:
Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. 46 - Ji-Yong An, Lei Zhang, Yong Zhou, Yu-Jun Zhao, Da-Fu Wang:
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information. 47 - Jaroslaw Polanski, Aleksandra Tkocz, Urszula Kucia:
Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships. 49 - Alioune Schurz, Bo-Han Su, Yi-shu Tu, Tony Tsung-Yu Lu, Olivia A. Lin, Yufeng J. Tseng:
G.A.M.E.: GPU-accelerated mixture elucidator. 50 - Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki:
A review of parameters and heuristics for guiding metabolic pathfinding. 51 - Patrick J. Ropp, Aaron J. Friedman, Jacob D. Durrant:
Scoria: a Python module for manipulating 3D molecular data. 52 - Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck:
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. 53 - Pierre Tremouilhac, An Nguyen, Yu-Chieh Huang, Serhii Kotov, Dominic Sebastian Lütjohann, Florian Hübsch, Nicole Jung, Stefan Bräse:
Chemotion ELN: an Open Source electronic lab notebook for chemists in academia. 54
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