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ORCIDJournal of Chemical Information and Modeling, Volume 59
Volume 59, Number 1, January 2019
- Thanh-Hoang Nguyen-Vo
, Tri Le, Duy Pham, Tri Nguyen, Phuc Le, An Nguyen, Thanh Nguyen, Thien-Ngan Nguyen, Vu Nguyen, Hai Do, Khang Trinh, Trong Hai Duong, Ly Le:
VIETHERB: A Database for Vietnamese Herbal Species. 1-9 - Mahendra Awale, Jean-Louis Reymond:
Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. 10-17 - Aoxiang Tao, Yuying Huang, Yasuhiro Shinohara, Matthew L. Caylor, Srinath Pashikanti, Dong Xu:
ezCADD: A Rapid 2D/3D Visualization-Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. 18-24 - Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimír Sládek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta:
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. 25-30 - Thomas Kainrad, Sascha Hunold, Thomas Seidel, Thierry Langer:
LigandScout Remote: A New User-Friendly Interface for HPC and Cloud Resources. 31-37 - Ying Yang, Amr H. Mahmoud, Markus A. Lill:
Modeling of Halogen-Protein Interactions in Co-Solvent Molecular Dynamics Simulations. 38-42 - Seokho Kang, Kyunghyun Cho:
Conditional Molecular Design with Deep Generative Models. 43-52 - Junmei Wang, Yubin Ge, Xiang-Qun Xie:
Development and Testing of Druglike Screening Libraries. 53-65 - Ruihan Zhang, Jing Lin, Yan Zou, Xing-Jie Zhang, Weilie Xiao:
Chemical Space and Biological Target Network of Anti-Inflammatory Natural Products. 66-73 - Fernanda I. Saldívar-González, Marilia Valli, Adriano D. Andricopulo, Vanderlan da Silva Bolzani, José L. Medina-Franco:
Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization. 74-85 - Michael González-Durruthy, Silvana Manske Nunes, Juliane Ventura-Lima, Marcos A. Gelesky, Humberto González Díaz, José Maria Monserrat, Riccardo Concu, M. Natália Dias Soeiro Cordeiro:
MitoTarget Modeling Using ANN-Classification Models Based on Fractal SEM Nano-Descriptors: Carbon Nanotubes as Mitochondrial F0F1-ATPase Inhibitors. 86-97 - Matthew P. Seddon, David A. Cosgrove, Martin J. Packer, Valerie J. Gillet:
Alignment-Free Molecular Shape Comparison Using Spectral Geometry: The Framework. 98-116 - Ruifeng Liu, Hao Wang, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist:
Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure-Activity Relationship Models Based on Deep Neural Networks? 117-126 - Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, Thomas Simonson, David Allouche:
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. 127-136 - Lucianna Helene Santos, Birgit J. Waldner, Julian E. Fuchs, Glaécia A. N. Pereira, Klaus R. Liedl, Ernesto Raúl Caffarena, Rafaela Salgado Ferreira:
Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. 137-148 - Andrea N. Bootsma, Steven E. Wheeler:
Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments. 149-158 - Shuheng Huang, Duo Zhang, Hu Mei, Muliadiyeremia Kevin, Sujun Qu, Xianchao Pan, Laichun Lu:
SMD-Based Interaction-Energy Fingerprints Can Predict Accurately the Dissociation Rate Constants of HIV-1 Protease Inhibitors. 159-169 - Lingling Zhang, Jianfen Fan, Mengnan Qu:
MD Simulations on the Transport Behaviors of Mixed Na+ and Li+ in a Transmembrane Cyclic Peptide Nanotube under an Electric Field. 170-180 - Ruifeng Liu, Anders Wallqvist:
Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds. 181-189 - Stavros Chatzieleftheriou, Stefanos Anogiannakis, Doros N. Theodorou, Nikos D. Lagaros:
SimNano: A Trust Region Strategy for Large-Scale Molecular Systems Energy Minimization Based on Exact Second-Order Derivative Information. 190-205 - Antoine Marion, Hatice Gokcan, Gerald Monard:
Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package. 206-214 - Fang-Yu Lin, Alexander D. MacKerell Jr.:
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. 215-228 - Kristian Kríz, Jan Rezác:
Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7. 229-235 - Callum J. Dickson, Viktor Hornak, Dallas Bednarczyk, José S. Duca:
Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules. 236-244 - Stefan M. Ivanov, Roland G. Huber, Irfan Alibay, Jim Warwicker, Peter J. Bond:
Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway. 245-261 - Ernesto Quintas-Sánchez, Richard Dawes:
AUTOSURF: A Freely Available Program To Construct Potential Energy Surfaces. 262-271 - Xiao Liu, Long Peng, John Z. H. Zhang:
Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. 272-281 - Shengchao Liu, Moayad Alnammi, Spencer S. Ericksen, Andrew F. Voter, Gene E. Ananiev, James L. Keck, F. Michael Hoffmann, Scott A. Wildman, Anthony Gitter:
Practical Model Selection for Prospective Virtual Screening. 282-293 - Jagna Witek, Shuzhe Wang, Benjamin Schroeder, Robin Lingwood, Andreas Dounas, Hans-Jörg Roth, Marianne Fouché, Markus Blatter, Oliver Lemke, Bettina G. Keller, Sereina Riniker:
Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. 294-308 - Srinivasaraghavan Kannan, Daniel Shao-Weng Tan, Chandra Shekhar Verma:
Effects of Single Nucleotide Polymorphisms on the Binding of Afatinib to EGFR: A Potential Patient Stratification Factor Revealed by Modeling Studies. 309-315 - Lanxuan Liu, Shuobing Fan, Wenjuan Li, Wentao Tao, Ting Shi, Yi-Lei Zhao:
Theoretical Investigation of the Structural Characteristics in the Active State of Akt1 Kinase. 316-325 - Subramani Karthikeyan, Ganesan Bharanidharan, Sriram Ragavan, Saravanan Kandasamy, Shanmugavel Chinnathambi, Kanniyappan Udayakumar, Rajendiran Mangaiyarkarasi, Anandh Sundaramoorthy, Prakasarao Aruna, Singaravelu Ganesan:
Comparative Binding Analysis ofN-Acetylneuraminic Acid in Bovine Serum Albumin and Humanα -1 Acid Glycoprotein. 326-338 - Cheng-Dong Li, Muhammad Junaid, Hui Chen, Arif Ali, Dong-Qing Wei:
Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations. 339-350 - Angelo Spinello, Elena Vecile, Antonio Abbate, Aldo Dobrina, Alessandra Magistrato:
How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways? 351-359 - Ping Xie, Si-Kao Guo, Hong Chen:
ATP-Concentration- and Force-Dependent Chemomechanical Coupling of Kinesin Molecular Motors. 360-372 - Khuraijam Dhanachandra Singh, Hamiyet Unal, Russell Desnoyer, Sadashiva S. Karnik:
Mechanism of Hormone Peptide Activation of a GPCR: Angiotensin II Activated State of AT1R Initiated by van der Waals Attraction. 373-385 - Philipp Nicolas Depta, Uwe Jandt, Maksym Dosta, An-Ping Zeng, Stefan Heinrich:
Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method. 386-398 - Zhicheng Zuo, Jin Liu:
Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease. 399-408 - Ruxi Qi, Ray Luo:
Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. 409-420 - Dimas Suárez, Natalia Díaz:
Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods. 421-440 - Laia Julió Plana, Alejandro D. Nadra, Dario A. Estrin, F. Javier Luque, Luciana Capece:
Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. 441-452 - Zheng Zhao, Lei Xie, Philip E. Bourne:
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. 453-462 - Francois Berenger, Yoshihiro Yamanishi:
A Distance-Based Boolean Applicability Domain for Classification of High Throughput Screening Data. 463-476 - Alexios Koutsoukas, George Chang, Christopher E. Keefer:
In-Silico Extraction of Design Ideas Using MMPA-by-QSAR and its Application on ADME Endpoints. 477-485 - Youyi Peng, Hiep Dong, William J. Welsh:
Comprehensive 3D-QSAR Model Predicts Binding Affinity of Structurally Diverse Sigma 1 Receptor Ligands. 486-497 - Muhammad Junaid, Muhammad Tahir Khan, Shaukat Iqbal Malik, Dong-Qing Wei:
Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N. 498-508 - Jonas Dittrich, Denis Schmidt, Christopher Pfleger, Holger Gohlke:
Converging a Knowledge-Based Scoring Function: DrugScore2018. 509-521 - Ting Ran, Wenjuan Li, Bingling Peng, Binglan Xie, Tao Lu, Shuai Lu, Wen Liu:
Virtual Screening with a Structure-Based Pharmacophore Model to Identify Small-Molecule Inhibitors of CARM1. 522-534 - Doris A. Schuetz, Mattia Bernetti, Martina Bertazzo, Djordje Musil, Hans-Michael Eggenweiler, Maurizio Recanatini, Matteo Masetti, Gerhard F. Ecker, Andrea Cavalli:
Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. 535-549 - Majid Jafari, Farahnoosh Doustdar, Faramarz Mehrnejad:
Molecular Self-Assembly Strategy for Encapsulation of an Amphipathicα -Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles. 550-563 - Iuri Casciuc, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Jürgen Bajorath, Alexandre Varnek:
Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? 564-572 - Viet-Khoa Tran-Nguyen, Franck Da Silva, Guillaume Bret, Didier Rognan:
All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening. 573-585 - Domenico Alberga, Daniela Trisciuzzi, Michele Montaruli, Francesco Leonetti, Giuseppe Felice Mangiatordi, Orazio Nicolotti:
A New Approach for Drug Target and Bioactivity Prediction: The Multifingerprint Similarity Search Algorithm (MuSSeL). 586-596 - Xiaoli An, Shaoyong Lu, Kun Song, Qiancheng Shen, Meilan Huang, Xiaojun Yao, Huanxiang Liu, Jian Zhang:
Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? 597-604 - Alexander S. Kirpich, Mukundan Ragavan, James A. Bankson, Lauren M. McIntyre, Matthew E. Merritt:
Kinetic Analysis of Hepatic Metabolism Using Hyperpolarized Dihydroxyacetone. 605-614 - Li Xue, Bin Tang, Wei Chen, Jiesi Luo:
Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network. 615-624
Volume 59, Number 2, February 2019
- Aleksandra I. Jarmolinska, Qin Zhou, Joanna I. Sulkowska, Faruck Morcos:
DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings. 625-629 - Chen-Yang Jia, Fan Wang, Ge-Fei Hao, Guangfu Yang:
InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules. 630-635 - Johannes Heidrich, Thomas E. Exner, Frank M. Boeckler:
Predicting the Magnitude ofσ -Holes Using VmaxPred, a Fast and Efficient Tool Supporting the Application of Halogen Bonds in Drug Discovery. 636-643 - Niek van Hilten, Florent Chevillard, Peter Kolb:
Virtual Compound Libraries in Computer-Assisted Drug Discovery. 644-651 - Qi Qi, Masahiko Taniguchi, Jonathan S. Lindsey:
Heuristics from Modeling of Spectral Overlap in Förster Resonance Energy Transfer (FRET). 652-667 - Lara Kuhnke, Antonius ter Laak, Andreas H. Göller:
Mechanistic Reactivity Descriptors for the Prediction of Ames Mutagenicity of Primary Aromatic Amines. 668-672 - Javier L. Baylon, Nicholas A. Cilfone, Jeffrey R. Gulcher, Thomas W. Chittenden:
Enhancing Retrosynthetic Reaction Prediction with Deep Learning Using Multiscale Reaction Classification. 673-688 - Benjamin P. Brown, Jeffrey L. Mendenhall, Jens Meiler:
BCL: : MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. 689-701 - David A. Dreier, Nancy D. Denslow, Christopher J. Martyniuk:
Computational in Vitro Toxicology Uncovers Chemical Structures Impairing Mitochondrial Membrane Potential. 702-712 - Alexey Lagunin, Athina Geronikaki, Phaedra Eleftheriou, Pavel V. Pogodin, Alexey V. Zakharov:
Rational Use of Heterogeneous Data in Quantitative Structure-Activity Relationship (QSAR) Modeling of Cyclooxygenase/Lipoxygenase Inhibitors. 713-730 - Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey:
Conformator: A Novel Method for the Generation of Conformer Ensembles. 731-742 - Rasmus Leth, Bogac Ercig, Lars Olsen, Flemming Steen Jørgensen:
Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants. 743-753 - Joel Wahl, Martin Smiesko:
Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. 754-765 - Thi Chinh Ngo, Thi Hau Nguyen, Duy Quang Dao:
Radical Scavenging Activity of Natural-Based Cassaine Diterpenoid Amides and Amines. 766-776 - Xiaoyan Zhou, Fangqiang Zhu:
Calculating Single-Channel Permeability and Conductance from Transition Paths. 777-785 - Tiago M. C. Simões, Abel João Padrão Gomes:
CavVis - A Field-of-View Geometric Algorithm for Protein Cavity Detection. 786-796 - Silvestre Massimo Modestia, Matheus Malta de Sá, Eric Auger, Gustavo Henrique Goulart Trossini, José Eduardo Krieger, Carlota de Oliveira Rangel-Yagui:
Biased Agonist TRV027 Determinants in AT1R by Molecular Dynamics Simulations. 797-808 - Rodrigo Cossio-Pérez, Gustavo Pierdominici-Sottile, Pablo Sobrado, Juliana Palma:
Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. 809-817 - Stefano Della-Longa, Alessandro Arcovito:
Microswitches for the Activation of the Nociceptin Receptor Induced by Cebranopadol: Hints from Microsecond Molecular Dynamics. 818-831 - Ge Qu, Mingxing Fu, Lili Zhao, Beibei Liu, Pi Liu, Wenchao Fan, Jun-An Ma, Zhoutong Sun:
Computational Insights into the Catalytic Mechanism of Bacterial Carboxylic Acid Reductase. 832-841 - Ye Jin, Mojie Duan, Xuwen Wang, Xiaotian Kong, Wenfang Zhou, Huiyong Sun, Hui Liu, Dan Li, Huidong Yu, Youyong Li, Tingjun Hou:
Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. 842-857 - Ning Tang, Budheswar Dehury, Kasper P. Kepp:
Computing the Pathogenicity of Alzheimer's Disease Presenilin 1 Mutations. 858-870 - Orkid Coskuner-Weber, Vladimir N. Uversky:
Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β 42. 871-884 - Andreas Lange, Johannes Heidrich, Markus O. Zimmermann, Thomas E. Exner, Frank M. Boeckler:
Scaffold Effects on Halogen Bonding Strength. 885-894 - Minyi Su, Qifan Yang, Yu Du, Guoqin Feng, Zhihai Liu, Yan Li, Renxiao Wang:
Comparative Assessment of Scoring Functions: The CASF-2016 Update. 895-913 - Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu:
Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. 914-923 - Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. 924-930 - Theodore L. Fobe, Andrei F. Kazakov, Demian Riccardi:
Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. 931-943 - Bing Xie, John D. Clark, David D. L. Minh:
Correction to "Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles". 944
Volume 59, Number 3, March 2019
- Günter Klambauer, Sepp Hochreiter, Matthias Rarey:
Machine Learning in Drug Discovery. 945-946 - Jochen Sieg, Florian Flachsenberg, Matthias Rarey:
In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. 947-961 - Noé Sturm, Jiangming Sun, Yves Vandriessche, Andreas Mayr, Günter Klambauer, Lars Carlsson, Ola Engkvist, Hongming Chen:
Application of Bioactivity Profile-Based Fingerprints for Building Machine Learning Models. 962-972 - Lixia Sun, Hongbin Yang, Yingchun Cai, Weihua Li, Guixia Liu, Yun Tang:
In Silico Prediction of Endocrine Disrupting Chemicals Using Single-Label and Multilabel Models. 973-982 - Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath:
Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling. 983-992 - Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath:
Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction. 993-1004 - Yadi Zhou, Suntara Cahya, Steven A. Combs, Christos A. Nicolaou, Ji-Bo Wang, Prashant V. Desai, Jie Shen:
Exploring Tunable Hyperparameters for Deep Neural Networks with Industrial ADME Data Sets. 1005-1016 - Joshua Staker, Kyle Marshall, Robert Abel, Carolyn McQuaw:
Molecular Structure Extraction from Documents Using Deep Learning. 1017-1029 - Conrad Stork, Ya Chen, Martin Sícho, Johannes Kirchmair:
Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. 1030-1043 - Xiuming Li, Xin Yan, Qiong Gu, Huihao Zhou, Di Wu, Jun Xu:
DeepChemStable: Chemical Stability Prediction with an Attention-Based Graph Convolution Network. 1044-1049 - Nobuaki Yasuo, Masakazu Sekijima:
Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning. 1050-1061 - Sergey Sosnin, Dmitry Karlov, Igor V. Tetko, Maxim V. Fedorov:
Comparative Study of Multitask Toxicity Modeling on a Broad Chemical Space. 1062-1072 - Chuipu Cai, Pengfei Guo, Yadi Zhou, Jingwei Zhou, Qi Wang, Fengxue Zhang, Jiansong Fang, Feixiong Cheng:
Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity. 1073-1084 - Yingchun Cai, Hongbin Yang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
Computational Prediction of Site of Metabolism for UGT-Catalyzed Reactions. 1085-1095 - Nathan Brown, Marco Fiscato, Marwin H. S. Segler, Alain C. Vaucher:
GuacaMol: Benchmarking Models for de Novo Molecular Design. 1096-1108 - Deyani Nocedo-Mena, Carlos Cornelio, María del Rayo Camacho-Corona, Elvira Garza-González, Noemi Waksman de Torres, Sonia Arrasate, Nuria Sotomayor, Esther Lete, Humberto González Díaz:
Modeling Antibacterial Activity with Machine Learning and Fusion of Chemical Structure Information with Microorganism Metabolic Networks. 1109-1120 - Eleni E. Litsa, Matthew I. Peña, Mark Moll, George Giannakopoulos, George N. Bennett, Lydia E. Kavraki:
Machine Learning Guided Atom Mapping of Metabolic Reactions. 1121-1135 - Peter Pogány, Navot Arad, Sam Genway, Stephen D. Pickett:
De Novo Molecule Design by Translating from Reduced Graphs to SMILES. 1136-1146 - Stephanie A. Brocke, Alexandra Degen, Alexander D. MacKerell Jr., Bercem Dutagaci, Michael Feig:
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. 1147-1162 - Markus Hofmarcher, Elisabeth Rumetshofer, Djork-Arné Clevert, Sepp Hochreiter, Günter Klambauer:
Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks. 1163-1171 - José Jiménez, Davide Sabbadin, Alberto Cuzzolin, Gerard Martínez-Rosell, Jacob Gora, John Manchester, José S. Duca, Gianni De Fabritiis:
PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks. 1172-1181