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Journal 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
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
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
The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability. 7:1-7:11 - Marcus Johansson
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
Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data. 12:1-12:11 - George van den Driessche
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
Modeling framework for isotopic labeling of heteronuclear moieties. 14:1-14:11 - Marco Capuccini
Large-scale virtual screening on public cloud resources with Apache Spark. 15:1-15:6 - Takako Takeda, Ming Hao
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. 16:1-16:9 - Jiangming Sun, Nina Jeliazkova
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. 17:1-17:9 - Steve O'Hagan
Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. 18:1-18:17 - Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka
Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. 19:1-19:12 - Milan Vorsilák
Nonpher: computational method for design of hard-to-synthesize structures. 20:1-20:7 - Hyoungrae Kim, Cheongyun Jang, Dharmendra Kumar Yadav
The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix. 21:1-21:26 - Emma Schymanski
Critical Assessment of Small Molecule Identification 2016: automated methods. 22:1-22:21 - Philipp-Maximilian Jacob
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
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
ChemSAR: an online pipelining platform for molecular SAR modeling. 27:1-27:13 - Till Schäfer
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
CPANNatNIC software for counter-propagation neural network to assist in read-across. 30:1-30:15 - Samantha Kanza
Electronic lab notebooks: can they replace paper? 31:1-31:15 - Ivana Blazenovic
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
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. 33:1-33:19 - Omer Kaspi, Abraham Yosipof
RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells. 34:1-34:15 - José R. Valdés-Martiní, Yovani Marrero-Ponce
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
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery. 38:1-38:14 - German A. Preciat Gonzalez
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. 39:1-39:15 - Rajarshi Guha
Helping to improve the practice of cheminformatics. 40:1-40:2 - Jiangming Sun, Nina Jeliazkova, Vladimir I. Chupakhin, José Felipe Golib Dzib, Ola Engkvist
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
Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR. 43:1-43:19 - Marcus Olivecrona
Molecular de-novo design through deep reinforcement learning. 48:1-48:14 - Marcus D. Hanwell
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application. 55:1-55:10 - Andrius Merkys
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
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. 58:1-58:13 - Yumeng Yan, Di Zhang
Efficient conformational ensemble generation of protein-bound peptides. 59:1-59:13 - Francois Berenger
Consensus queries in ligand-based virtual screening experiments. 60:1-60:13 - Antony J. Williams
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
BoBER: web interface to the base of bioisosterically exchangeable replacements. 62:1-62:8 - Samuel Boobier
Can human experts predict solubility better than computers? 63:1-63:14 - Mathilde Koch
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
Systematic exploration of multiple drug binding sites. 65:1-65:12 - Ting Feng, Fu Chen, Yu Kang
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
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
Efficiency of different measures for defining the applicability domain of classification models. 44 - Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers
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
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information. 47 - Jaroslaw Polanski
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
A review of parameters and heuristics for guiding metabolic pathfinding. 51 - Patrick J. Ropp
Scoria: a Python module for manipulating 3D molecular data. 52 - Egon L. Willighagen
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. 53 - Pierre Tremouilhac
Chemotion ELN: an Open Source electronic lab notebook for chemists in academia. 54
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