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ORCIDJournal of Cheminformatics, Volume 10
Volume 10, Number 1, December 2018
- Samina Kausar
, André O. Falcão:
An automated framework for QSAR model building. 1:1-1:23 - Sehan Lee, Mace G. Barron:
3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein-ligand interactions. 2:1-2:13 - George van den Driessche, Denis Fourches:
Adverse drug reactions triggered by the common HLA-B*57: 01 variant: virtual screening of DrugBank using 3D molecular docking. 3:1-3:24 - Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita, Tatsuya Takagi:
Mordred: a molecular descriptor calculator. 4:1-4:14 - James G. Moberly, Matthew T. Bernards, Kristopher V. Waynant:
Key features and updates for origin 2018. 5:1-5:2 - Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki, Jacob D. Durrant:
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. 6:1-6:9 - Fredrik Svensson, Avid M. Afzal, Ulf Norinder, Andreas Bender:
Maximizing gain in high-throughput screening using conformal prediction. 7:1-7:10 - Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Zubair Toor, Wesley Schaal, Erwin Laure, Ola Spjuth:
Efficient iterative virtual screening with Apache Spark and conformal prediction. 8:1-8:8 - Rafaela Gladysz, Fábio Mendes dos Santos, Wilfried Langenaeker, Gert Thijs, Koen Augustyns, Hans De Winter:
Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening. 9:1-9:24 - Kamel Mansouri, Christopher M. Grulke, Richard S. Judson, Antony J. Williams:
OPERA models for predicting physicochemical properties and environmental fate endpoints. 10:1-10:19 - Pieter P. Plehiers, Guy B. Marin, Christian V. Stevens, Kevin M. Van Geem:
Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics. 11:1-11:18 - Abid Qureshi, Akanksha Rajput, Gazaldeep Kaur, Manoj Kumar:
HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors. 12:1-12:15 - Martin Sícho, Milan Vorsilák, Daniel Svozil:
Comment on "The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability". 13:1-13:2 - Hans De Winter, Julio Cesar Dias Lopes:
Reply to the comment made by Šicho, Vorśilák and Svozil on 'The Power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability'. 14:1-14:2 - Julia B. Jasper, Lina Humbeck, Tobias Brinkjost, Oliver Koch:
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening. 15:1-15:13 - Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen, Dong-Sheng Cao:
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions. 16:1-16:11 - Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson, Ola Spjuth:
A confidence predictor for logD using conformal regression and a support-vector machine. 17:1-17:10 - Vishwesh Venkatraman, Rajesh Raju, Solon P. Oikonomopoulos, Bjørn K. Alsberg:
The dye-sensitized solar cell database. 18:1-18:9 - Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler:
Finding the K best synthesis plans. 19:1-19:21 - Aeri Lee, Seungpyo Hong, Dongsup Kim:
KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking. 20:1-20:10 - Tianyi Qiu, Dingfeng Wu, Jingxuan Qiu, Zhiwei Cao:
Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling. 21:1-21:9 - Guenter Grethe, Gerd Blanke, Hans Kraut, Jonathan M. Goodman:
International chemical identifier for reactions (RInChI). 22:1-22:9 - Miguel Quirós, Saulius Grazulis, Saule Girdzijauskaite, Andrius Merkys, Antanas Vaitkus:
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database. 23:1-23:17 - Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Sachem: a chemical cartridge for high-performance substructure search. 27:1-27:11 - Jie Dong, Ning-Ning Wang, Zhi-Jiang Yao, Lin Zhang, Yan Cheng, Defang Ouyang, Ai-Ping Lu, Dong-Sheng Cao:
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. 29:1-29:11 - Jia Qu, Xing Chen, Ya-Zhou Sun, Jian-Qiang Li, Zhong Ming:
Inferring potential small molecule-miRNA association based on triple layer heterogeneous network. 30:1-30:14 - Jaechang Lim, Seongok Ryu, Jin Woo Kim, Woo Youn Kim:
Molecular generative model based on conditional variational autoencoder for de novo molecular design. 31:1-31:9 - Obdulia Rabal, Andrea Castellar, Julen Oyarzabal:
Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization. 32:1-32:19 - Yibo Li, Liangren Zhang, Zhenming Liu:
Multi-objective de novo drug design with conditional graph generative model. 33:1-33:24 - Ning-Ning Wang, Jie Dong, Lin Zhang, Defang Ouyang, Yan Cheng, Alex F. Chen, Ai-Ping Lu, Dong-Sheng Cao:
HAMdb: a database of human autophagy modulators with specific pathway and disease information. 34:1-34:8 - Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub, Achim Zielesny:
SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation. 35:1-35:10 - Volker Hähnke, Sunghwan Kim, Evan Bolton:
PubChem chemical structure standardization. 36:1-36:40 - Paul Thompson, Sophia Daikou, Kenju Ueno, Riza Batista-Navarro, Jun'ichi Tsujii, Sophia Ananiadou:
Annotation and detection of drug effects in text for pharmacovigilance. 37:1-37:33 - Serhii Kotov, Pierre Tremouilhac, Nicole Jung, Stefan Bräse:
Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications. 38:1-38:8 - Radoslav Krivák, David Hoksza:
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. 39:1-39:12 - Yuezhou Zhang, Henri Xhaard, Leo Ghemtio:
Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors. 40:1-40:16 - Robert J. Allaway, Salvatore La Rosa, Justin Guinney, Sara J. C. Gosline:
Probing the chemical-biological relationship space with the Drug Target Explorer. 41:1-41:14 - Nikolay T. Kochev, Svetlana Avramova, Nina Jeliazkova:
Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation. 42:1-42:29 - Florbela Pereira, João Aires-de-Sousa:
Machine learning for the prediction of molecular dipole moments obtained by density functional theory. 43:1-43:11 - Richard Marchese Robinson, Kevin J. Roberts, Elaine B. Martin:
The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility. 44:1-44:21 - Andrew D. McEachran, Kamel Mansouri, Christopher M. Grulke, Emma Schymanski, Christoph Ruttkies, Antony J. Williams:
"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies. 45:1-45:16 - Ola Spjuth:
Novel applications of Machine Learning in cheminformatics. 46:1-46:2 - Ilya A. Balabin, Richard S. Judson:
Exploring non-linear distance metrics in the structure-activity space: QSAR models for human estrogen receptor. 47:1-47:11 - Anita Rácz, Dávid Bajusz, Károly Héberger:
Life beyond the Tanimoto coefficient: similarity measures for interaction fingerprints. 48:1-48:12 - Alexander Kensert, Jonathan Alvarsson, Ulf Norinder, Ola Spjuth:
Evaluating parameters for ligand-based modeling with random forest on sparse data sets. 49:1-49:10 - Ming Hao, Stephen H. Bryant, Yanli Wang:
A new chemoinformatics approach with improved strategies for effective predictions of potential drugs. 50:1-50:9 - César R. García-Jacas, Lisset Cabrera-Leyva, Yovani Marrero-Ponce, José Suárez-Lezcano, Fernando Cortés-Guzmán, Mario Pupo-Meriño, Ricardo Vivas-Reyes:
Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs). 51:1-51:17 - Yasemin Yesiltepe, Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Mark I. Borkum, Patrick Reardon, Nancy M. Washton, Thomas O. Metz, Justin G. Teeguarden, Niranjan Govind, Ryan S. Renslow:
An automated framework for NMR chemical shift calculations of small organic molecules. 52:1-52:16 - Phyo Phyo Kyaw Zin, Gavin Williams, Denis Fourches:
Cheminformatics-based enumeration and analysis of large libraries of macrolide scaffolds. 53:1-53:20 - Mariam Pirashvili, Lee Steinberg, Francisco Belchí Guillamón, Mahesan Niranjan, Jeremy G. Frey, Jacek Brodzki:
Improved understanding of aqueous solubility modeling through topological data analysis. 54:1-54:14 - Norberto Sánchez-Cruz, José L. Medina-Franco:
Statistical-based database fingerprint: chemical space dependent representation of compound databases. 55:1-55:13 - Raghuram Srinivas, Pavel V. Klimovich, Eric C. Larson:
Implicit-descriptor ligand-based virtual screening by means of collaborative filtering. 56:1-56:20 - Jeremy R. Ash, Jacqueline M. Hughes-Oliver:
chemmodlab: a cheminformatics modeling laboratory R package for fitting and assessing machine learning models. 57:1-57:20 - Francisco M. Couto, Andre Lamurias:
MER: a shell script and annotation server for minimal named entity recognition and linking. 58:1-58:10 - Peter Corbett, John Boyle:
Chemlistem: chemical named entity recognition using recurrent neural networks. 59:1-59:9 - Domenico Gadaleta, Anna Lombardo, Cosimo Toma, Emilio Benfenati:
A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications. 60:1-60:13 - Jeffrey Plante, Stéphane Werner:
JPlogP: an improved logP predictor trained using predicted data. 61:1-61:10 - Hio Kuan Tai, Siti Azma Jusoh, Shirley W. I. Siu:
Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. 62:1-62:13 - Johannes Kirschnick, Philippe Thomas, Roland Roller, Leonhard Hennig:
SIA: a scalable interoperable annotation server for biomedical named entities. 63:1-63:7 - Po-Ting Lai, Ming-Siang Huang, Ting-Hao Yang, Wen-Lian Hsu, Richard Tzong-Han Tsai:
Statistical principle-based approach for gene and protein related object recognition. 64:1-64:9 - Ling Luo, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Jian Wang, Hongfei Lin:
A neural network approach to chemical and gene/protein entity recognition in patents. 65:1-65:10 - Daniel Probst, Jean-Louis Reymond:
A probabilistic molecular fingerprint for big data settings. 66:1-66:12 - Frédéric Wieber, Alejandro Pisanty, Alexandre Hocquet:
"We were here before the Web and hype...": a brief history of and tribute to the Computational Chemistry List. 67:1-67:3 - Sérgio Matos:
Configurable web-services for biomedical document annotation. 68:1-68:9 - Anurag Passi, Neeraj Rajput, David J. Wild, Anshu Bhardwaj:
RepTB: a gene ontology based drug repurposing approach for tuberculosis. 24 - Karina van den Broek, Hubert Kuhn, Achim Zielesny:
Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics. 25 - Antonio de la Vega de León, Beining Chen, Valerie J. Gillet:
Effect of missing data on multitask prediction methods. 26 - Ilia Korvigo, Maxim Holmatov, Anatolii Zaikovskii, Mikhail Skoblov:
Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules. 28
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