From 9ccccd6e408b610c99c9351c7bd2ae91a7a96067 Mon Sep 17 00:00:00 2001
From: Merle Stahl <merle.stahl@studium.uni-hamburg.de>
Date: Wed, 19 Jan 2022 15:13:15 +0100
Subject: [PATCH] Layout
---
assets/{cn.js => cn_default.js} | 3 +-
assets/{cn2.js => cn_timeline.js} | 5 +-
assets/index.html | 4 +-
assets/json_text.json | 840 ++++++++++++++++++++++++++++--
4 files changed, 789 insertions(+), 63 deletions(-)
rename assets/{cn.js => cn_default.js} (99%)
rename assets/{cn2.js => cn_timeline.js} (99%)
diff --git a/assets/cn.js b/assets/cn_default.js
similarity index 99%
rename from assets/cn.js
rename to assets/cn_default.js
index f85532d..d4e0d41 100644
--- a/assets/cn.js
+++ b/assets/cn_default.js
@@ -120,7 +120,7 @@ var simulation = d3.forceSimulation()
else {return 70;}
}).strength(0.5))
.force("charge", d3.forceManyBody().strength(0.001))
- .force("center", d3.forceCenter(width/2, height/2+20))
+ .force("center", d3.forceCenter(width/2-20, height/2+20))
.force("yscale", d3.forceY().strength(function(d) {
if (d.group == "Input") {return 300;}
else {return 200;}
@@ -567,4 +567,3 @@ function svg_string_to_image( svgString, width, height, format, callback ) {
image.src = imgsrc;
}
-
diff --git a/assets/cn2.js b/assets/cn_timeline.js
similarity index 99%
rename from assets/cn2.js
rename to assets/cn_timeline.js
index 9957ad2..9a5199d 100644
--- a/assets/cn2.js
+++ b/assets/cn_timeline.js
@@ -121,8 +121,9 @@ var simulation = d3.forceSimulation()
else {return 75;}
}).strength(1))
.force("charge", d3.forceManyBody().strength(0.001))
- .force("center", d3.forceCenter(width/2, height/2+20))
+ .force("center", d3.forceCenter(width/2-20, height/2+20))
.alpha(0.004)
+ .velocityDecay(0.65)
.on("end", zoom_to);
/**
@@ -159,6 +160,7 @@ d3.json("json_text.json").then(success,failure)
function success(graph){
update(graph.links, graph.nodes);
}
+
function failure(graph){
localStorage.setItem("oldjson","irgendwaswasimmergespeichertwirdwennkeinejsondaist")
}
@@ -610,4 +612,3 @@ function svg_string_to_image( svgString, width, height, format, callback ) {
image.src = imgsrc;
}
-
diff --git a/assets/index.html b/assets/index.html
index e69feb0..72477ea 100644
--- a/assets/index.html
+++ b/assets/index.html
@@ -155,7 +155,7 @@
var htmlHeader = document.getElementsByTagName("head")[0];
var myScript = document.createElement('script');
myScript.type = 'text/javascript';
- myScript.src = 'cn.js';
+ myScript.src = 'cn_default.js';
myScript.id='abc';
htmlHeader.appendChild(myScript);
}
@@ -164,7 +164,7 @@
var htmlHeader = document.getElementsByTagName("head")[0];
var myScript = document.createElement('script');
myScript.type = 'text/javascript';
- myScript.src = 'cn2.js';
+ myScript.src = 'cn_timeline.js';
myScript.id='abc';
htmlHeader.appendChild(myScript);
}
diff --git a/assets/json_text.json b/assets/json_text.json
index c023ef5..2effc53 100644
--- a/assets/json_text.json
+++ b/assets/json_text.json
@@ -1,114 +1,840 @@
{
"nodes": [
+ {
+ "doi": "https://doi.org/10.1021/ci980029a",
+ "name": "Prediction of Human Intestinal Absorption of Drug Compounds from Molecular Structure",
+ "author": [
+ "Matthew D. Wessel",
+ "Peter C. Jurs",
+ "John W. Tolan",
+ "Steven M. Muskal"
+ ],
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+ "journal": "J. Chem. Inf. Comput. Sci.",
+ "group": "Reference",
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+ },
+ {
+ "doi": "https://doi.org/10.1021/ci025620t",
+ "name": "Active Learning with Support Vector Machines in the Drug Discovery Process\u2021",
+ "author": [
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+ "Jun Liao",
+ "Gunnar R\u00e4tsch",
+ "Michael Mathieson",
+ "Santosh Putta",
+ "Christian Lemmen"
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+ "group": "Reference",
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+ "doi": "https://doi.org/10.1021/acs.jcim.5b00332",
+ "name": "Feasibility of Active Machine Learning for Multiclass Compound Classification",
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+ "Florian Flachsenberg",
+ "Ulrike von Luxburg",
+ "Matthias Rarey"
+ ],
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+ "group": "Reference",
+ "depth": 0,
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+ "name": "Rapid Discovery of a Novel Series of Abl Kinase Inhibitors by Application of an Integrated Microfluidic Synthesis and Screening Platform",
+ "author": [
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+ "Karen Dixon",
+ "Elizabeth Farrant",
+ "Qixing Feng",
+ "Karl R. Gibson",
+ "Willem P. van Hoorn",
+ "James Mills",
+ "Trevor Morgan",
+ "David M. Parry",
+ "Manoj K. Ramjee",
+ "Christopher N. Selway",
+ "Gary J. Tarver",
+ "Gavin Whitlock",
+ "Adrian G. Wright"
+ ],
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+ "journal": "J. Med. Chem. ",
+ "group": "Reference",
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+ },
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+ "doi": "https://doi.org/10.1021/ci700085q",
+ "name": "Virtual Screening System for Finding Structurally Diverse Hits by Active Learning",
+ "author": [
+ "Yukiko Fujiwara",
+ "Yoshiko Yamashita",
+ "Tsutomu Osoda",
+ "Minoru Asogawa",
+ "Chiaki Fukushima",
+ "Masaaki Asao",
+ "Hideshi Shimadzu",
+ "Kazuya Nakao",
+ "Ryo Shimizu"
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+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
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+ },
+ {
+ "doi": "https://doi.org/10.1021/acscentsci.7b00572",
+ "name": "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules",
+ "author": [
+ "Rafael G\u00f3mez-Bombarelli",
+ "Jennifer N. Wei",
+ "David Duvenaud",
+ "Jos\u00e9 Miguel Hern\u00e1ndez-Lobato",
+ "Benjam\u00edn S\u00e1nchez-Lengeling",
+ "Dennis Sheberla",
+ "Jorge Aguilera-Iparraguirre",
+ "Timothy D. Hirzel",
+ "Ryan P. Adams",
+ "Al\u00e1n Aspuru-Guzik"
+ ],
+ "year": "January 12, 2018",
+ "journal": "ACS Cent. Sci.",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 98
+ },
+ {
+ "doi": "https://doi.org/10.1021/ci700157b",
+ "name": "y-Randomization and Its Variants in QSPR/QSAR",
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+ "Christoph R\u00fccker",
+ "Gerta R\u00fccker",
+ "Markus Meringer"
+ ],
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+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 100
+ },
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+ "doi": "https://doi.org/10.1021/acscentsci.6b00367",
+ "name": "Low Data Drug Discovery with One-Shot Learning",
+ "author": [
+ "Han Altae-Tran",
+ "Bharath Ramsundar",
+ "Aneesh S. Pappu",
+ "Vijay Pande"
+ ],
+ "year": "April 3, 2017",
+ "journal": "ACS Cent. Sci.",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 100
+ },
+ {
+ "doi": "https://doi.org/10.1021/ci400737s",
+ "name": "QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem",
+ "author": [
+ "Alexey V. Zakharov",
+ "Megan L. Peach",
+ "Markus Sitzmann",
+ "Marc C. Nicklaus"
+ ],
+ "year": "February 13, 2014",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 74
+ },
+ {
+ "doi": "https://doi.org/10.1021/jm0608356",
+ "name": "Benchmarking Sets for Molecular Docking",
+ "author": [
+ "Niu Huang",
+ "Brian K. Shoichet",
+ "John J. Irwin"
+ ],
+ "year": "October 26, 2006",
+ "journal": "Journal of Medicinal Chemistry",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 100
+ },
+ {
+ "doi": "https://doi.org/10.1021/ci200528d",
+ "name": "Recognizing Pitfalls in Virtual Screening: A Critical Review",
+ "author": [
+ "Thomas Scior",
+ "Andreas Bender",
+ "Gary Tresadern",
+ "Jos\u00e9 L. Medina-Franco",
+ "Karina Mart\u00ednez-Mayorga",
+ "Thierry Langer",
+ "Karina Cuanalo-Contreras",
+ "Dimitris K. Agrafiotis"
+ ],
+ "year": "March 21, 2012",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 100
+ },
+ {
+ "doi": "https://doi.org/10.1021/jm025507u",
+ "name": "Docking into Knowledge-Based Potential Fields:\u2009 A Comparative Evaluation of DrugScore",
+ "author": [
+ "Christoph A. Sotriffer",
+ "Holger Gohlke",
+ "Gerhard Klebe"
+ ],
+ "year": "April 20, 2002",
+ "journal": "Journal of Medicinal Chemistry",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 72
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.accounts.6b00491",
+ "name": "Forging the Basis for Developing Protein\u2013Ligand Interaction Scoring Functions",
+ "author": [
+ "Zhihai Liu",
+ "Minyi Su",
+ "Li Han",
+ "Jie Liu",
+ "Qifan Yang",
+ "Yan Li",
+ "Renxiao Wang"
+ ],
+ "year": "February 9, 2017",
+ "journal": "Acc. Chem. Res.",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 100
+ },
+ {
+ "doi": "https://doi.org/10.1021/ci400510e",
+ "name": "Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction",
+ "author": [
+ "Michal Brylinski"
+ ],
+ "year": "October 30, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 35
+ },
+ {
+ "doi": "https://doi.org/10.1021/ci2003889",
+ "name": "NNScore 2.0: A Neural-Network Receptor\u2013Ligand Scoring Function",
+ "author": [
+ "Jacob D. Durrant",
+ "J. Andrew McCammon"
+ ],
+ "year": "October 22, 2011",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Reference",
+ "depth": 0,
+ "citations": 99
+ },
{
- "doi": "https://doi.org/10.1021/acs.jcim.5b00332",
- "name": "Feasibility of Active Machine Learning for Multiclass Compound Classification",
+ "doi": "https://doi.org/10.1021/acs.analchem.1c03508",
+ "name": "Explainable Deep Learning-Assisted Fluorescence Discrimination for Aminoglycoside Antibiotic Identification",
"author": [
- "Tobias Löang",
- "Florian Flachsenberg",
- "Ulrike von Luxburg",
- "Matthias Rarey"
+ "Xiaoqing Tan",
+ "Yongpeng Liang",
+ "Yingying Ye",
+ "Zhihao Liu",
+ "Jianxin Meng",
+ "Fengyu Li"
],
- "year": "January 7, 2016",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Input",
- "depth": 0,
- "citations": 5
+ "year": "January 3, 2022",
+ "journal": "Anal. Chem.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
},
{
- "doi": "https://doi.org/10.1021/acs.jcim.7b00729",
- "name": "Modeling Kinase Inhibition Using Highly Confident Data Sets",
+ "doi": "https://doi.org/10.1021/jacs.1c08211",
+ "name": "Self-Improving Photosensitizer Discovery System via Bayesian Search with First-Principle Simulations",
"author": [
- "Sorin Avram",
- "Alina Bora",
- "Liliana Halip",
- "Ramona Curp\u0103n"
+ "Shidang Xu",
+ "Jiali Li",
+ "Pengfei Cai",
+ "Xiaoli Liu",
+ "Bin Liu",
+ "Xiaonan Wang",
+ "Shengyong Yang"
],
- "year": "April 30, 2018",
- "journal": "Journal of Chemical Information and Modeling",
+ "year": "November 17, 2021",
+ "journal": "Journal of the American Chemical Society",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.joc.1c01242",
+ "name": "Application of an Electrochemical Microflow Reactor for Cyanosilylation: Machine Learning-Assisted Exploration of Suitable Reaction Conditions for Semi-Large-Scale Synthesis",
+ "author": [
+ "Eisuke Sato",
+ "Mayu Fujii",
+ "Hiroki Tanaka",
+ "Koichi Mitsudo",
+ "Masaru Kondo",
+ "Shinobu Takizawa",
+ "Hiroaki Sasai",
+ "Takeshi Washio",
+ "Kazunori Ishikawa",
+ "Seiji Suga"
+ ],
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+ "group": "Citedby",
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+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jmedchem.1c01788",
+ "name": "Back to the Medicinal Chemistry Future",
+ "author": [
+ "Mariateresa Giustiniano",
+ "Christian W. Gruber",
+ "Caitlin N. Kent",
+ "Paul C. Trippier"
+ ],
+ "year": "November 1, 2021",
+ "journal": "Journal of Medicinal Chemistry",
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+ },
+ {
+ "doi": "https://doi.org/10.1021/acscentsci.1c00535",
+ "name": "The Evolution of Data-Driven Modeling in Organic Chemistry",
+ "author": [
+ "Wendy L. Williams",
+ "Lingyu Zeng",
+ "Tobias Gensch",
+ "Matthew S. Sigman",
+ "Abigail G. Doyle",
+ "Eric V. Anslyn"
+ ],
+ "year": "October 19, 2021",
+ "journal": "ACS Cent. Sci.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jpclett.1c02477",
+ "name": "Size Doesn\u2019t Matter: Predicting Physico- or Biochemical Properties Based on Dozens of Molecules",
+ "author": [
+ "Kirill Karpov",
+ "Artem Mitrofanov",
+ "Vadim Korolev",
+ "Valery Tkachenko"
+ ],
+ "year": "September 16, 2021",
+ "journal": "J. Phys. Chem. Lett.",
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"depth": 1,
"citations": 0
},
{
- "doi": "https://doi.org/10.1021/acs.jcim.7b00729",
- "name": "Modeling Kinase Inhibition Using Highly Confident Data Sets",
+ "doi": "https://doi.org/10.1021/acs.jcim.1c00601",
+ "name": "SMINBR: An Integrated Network and Chemoinformatics Tool Specialized for Prediction of Two-Component Crystal Formation",
"author": [
- "Sorin Avram",
- "Alina Bora",
- "Liliana Halip",
- "Ramona Curp\u0103n"
+ "Lulu Zheng",
+ "Bin Zhu",
+ "Zengrui Wu",
+ "Fang Liang",
+ "Minghuang Hong",
+ "Guixia Liu",
+ "Weihua Li",
+ "Guobin Ren",
+ "Yun Tang"
],
- "year": "April 30, 2018",
+ "year": "August 26, 2021",
"journal": "Journal of Chemical Information and Modeling",
"group": "Citedby",
"depth": 1,
"citations": 0
},
{
- "doi": "https://doi.org/10.1021/acs.jcim.5b00646",
- "name": "Predictive Models for Fast and Effective Profiling of Kinase Inhibitors",
+ "doi": "https://doi.org/10.1021/acssensors.1c01600",
+ "name": "Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation",
"author": [
- "Alina Bora",
- "Sorin Avram",
- "Ionel Ciucanu",
- "Marius Raica",
- "Stefana Avram"
+ "Yi Tao",
+ "Lin Chen",
+ "Meiling Pan",
+ "Fei Zhu",
+ "Dong Zhu"
],
- "year": "April 11, 2016",
+ "year": "September 13, 2021",
+ "journal": "ACS Sens.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.chemrev.0c00749",
+ "name": "Machine Learning for Electronically Excited States of Molecules",
+ "author": [
+ "Julia Westermayr",
+ "Philipp Marquetand"
+ ],
+ "year": "November 19, 2020",
+ "journal": "Chem. Rev.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.1c00292",
+ "name": "True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better",
+ "author": [
+ "Viet-Khoa Tran-Nguyen",
+ "Guillaume Bret",
+ "Didier Rognan"
+ ],
+ "year": "June 10, 2021",
"journal": "Journal of Chemical Information and Modeling",
"group": "Citedby",
"depth": 1,
- "citations": 2
+ "citations": 0
},
{
- "doi": "https://doi.org/10.1021/acs.jcim.6b00709",
- "name": "Matched Molecular Series: Measuring SAR Similarity",
+ "doi": "https://doi.org/10.1021/acs.jcim.1c00086",
+ "name": "Balancing Data on Deep Learning-Based Proteochemometric Activity Classification",
"author": [
- "Emanuel S. R. Ehmki",
- "Christian Kramer"
+ "Angela Lopez-del Rio",
+ "Sergio Picart-Armada",
+ "Alexandre Perera-Lluna"
],
- "year": "May 1, 2017",
+ "year": "March 29, 2021",
"journal": "Journal of Chemical Information and Modeling",
- "group": "Input",
- "depth": 0,
- "citations": 5
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
},
{
- "doi": "https://doi.org/10.1021/acs.jcim.0c00269",
- "name": "Matched Molecular Series Analysis for ADME Property Prediction",
+ "doi": "https://doi.org/10.1021/acs.jcim.0c01143",
+ "name": "The Playbooks of Medicinal Chemistry Design Moves",
"author": [
"Mahendra Awale",
+ "J\u00e9r\u00f4me Hert",
+ "Laura Guasch",
"Sereina Riniker",
"Christian Kramer"
],
- "year": "May 5, 2020",
+ "year": "February 1, 2021",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.0c01046",
+ "name": "Machine Learning Enhanced Spectrum Recognition Based on Computer Vision (SRCV) for Intelligent NMR Data Extraction",
+ "author": [
+ "Wenqiang Jia",
+ "Zhuo Yang",
+ "Minjian Yang",
+ "Liang Cheng",
+ "Zengrong Lei",
+ "Xiaojian Wang"
+ ],
+ "year": "November 10, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acsbiomaterials.0c01459",
+ "name": "Satellite-Based Sensor for Environmental Heat-Stress Sweat Creatinine Monitoring: The Remote Artificial Intelligence-Assisted Epidermal Wearable Sensing for Health Evaluation",
+ "author": [
+ "Surachate Kalasin",
+ "Pantawan Sangnuang",
+ "Werasak Surareungchai"
+ ],
+ "year": "December 23, 2020",
+ "journal": "ACS Biomater. Sci. Eng.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.0c00565",
+ "name": "Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction",
+ "author": [
+ "Elena L. C\u00e1ceres",
+ "Nicholas C. Mew",
+ "Michael J. Keiser"
+ ],
+ "year": "November 27, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.0c01028",
+ "name": "Dipole Moment Variation Clears Up Electronic Excitations in the \u03c0-Stacked Complexes of Fluorescent Protein Chromophores",
+ "author": [
+ "Maria G. Khrenova",
+ "Fedor D. Mulashkin",
+ "Egor S. Bulavko",
+ "Tatiana M. Zakharova",
+ "Alexander V. Nemukhin"
+ ],
+ "year": "November 18, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design",
+ "author": [
+ "Ansgar Schuffenhauer",
+ "Nadine Schneider",
+ "Samuel Hintermann",
+ "Douglas Auld",
+ "Jutta Blank",
+ "Simona Cotesta",
+ "Caroline Engeloch",
+ "Nikolas Fechner",
+ "Christoph Gaul",
+ "Jerome Giovannoni",
+ "Johanna Jansen",
+ "John Joslin",
+ "Philipp Krastel",
+ "Eugen Lounkine",
+ "John Manchester",
+ "Lauren G. Monovich",
+ "Anna Paola Pelliccioli",
+ "Manuel Schwarze",
+ "Michael D. Shultz",
+ "Nikolaus Stiefl",
+ "Daniel K. Baeschlin"
+ ],
+ "year": "November 3, 2020",
+ "journal": "Journal of Medicinal Chemistry",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jpclett.0c02836",
+ "name": "COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2",
+ "author": [
+ "Sergey Gusarov",
+ "Stanislav R. Stoyanov"
+ ],
+ "year": "October 26, 2020",
+ "journal": "J. Phys. Chem. Lett.",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 0
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.0c00155",
+ "name": "LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening",
+ "author": [
+ "Viet-Khoa Tran-Nguyen",
+ "C\u00e9lien Jacquemard",
+ "Didier Rognan"
+ ],
+ "year": "April 13, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "group": "Citedby",
+ "depth": 1,
+ "citations": 1
+ },
+ {
+ "doi": "https://doi.org/10.1021/acs.jcim.9b01212",
+ "name": "Predicting Binding from Screening Assays with Transformer Network Embeddings",
+ "author": [
+ "Paul Morris",
+ "Rachel St. Clair",
+ "William Edward Hahn",
+ "Elan Barenholtz"
+ ],
+ "year": "June 22, 2020",
"journal": "Journal of Chemical Information and Modeling",
"group": "Citedby",
"depth": 1,
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--
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