From 6d338c38b922c588ad709f2a444ee1d34dd95c76 Mon Sep 17 00:00:00 2001
From: Merle Stahl <merle.stahl@studium.uni-hamburg.de>
Date: Fri, 10 Dec 2021 12:21:18 +0100
Subject: [PATCH] an Graph zoomen
---
Output/Graph/cn.js | 129 ++++-
Output/Graph/json_text.json | 512 +++++++++++++++----
Output/Graph/json_text_version1.json | 437 ++++++++++++++++
Output/Graph/json_text_version2.json | 437 ++++++++++++++++
Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js | 61 ++-
Output/Graph_mit_Zeitstrahl/json_text.json | 512 +++++++++++++++----
6 files changed, 1821 insertions(+), 267 deletions(-)
create mode 100644 Output/Graph/json_text_version1.json
create mode 100644 Output/Graph/json_text_version2.json
diff --git a/Output/Graph/cn.js b/Output/Graph/cn.js
index a1f6ea8..9a985e0 100644
--- a/Output/Graph/cn.js
+++ b/Output/Graph/cn.js
@@ -19,10 +19,10 @@ var textabstract='';
var node,
r=10,
color = d3.scaleOrdinal()
- .domain(["citing", "input", "cited"])
+ .domain(["height", "input", "depth"])
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
yscale = d3.scaleOrdinal()
- .domain(["citing", "input", "cited"])
+ .domain(["height", "input", "depth"])
.range([0, 200, 400]),
linetype=d3.scaleOrdinal()
.domain(["line","dotted"])
@@ -105,11 +105,13 @@ legendarrow.append("text")
state of the layout has changed (simulation has advanced by a tick)
*/
var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(100).strength(1))
- .force("collide", d3.forceCollide(50))
- .force("charge", d3.forceManyBody().strength(-30))
- .force("center", d3.forceCenter(width/2, height/2))
- .force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}));
+ .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(200))
+ .force("collide", d3.forceCollide(50).strength(0.5))
+ .force("charge", d3.forceManyBody())
+ .force("center", d3.forceCenter(width/2, height/2+20))
+ .force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}))
+ .alpha(0.1);
+
/**
* creates group element
@@ -142,8 +144,84 @@ function update(links, nodes) {
link.attr('marker-end', function(d) {return updateMarker("#999", d.target);})
.style("stroke-dasharray",function(d){return self_cit(d.source,d.target)? ("8,8"): ("1,0")});
+
+ zoomTo();
}
+
+function zoomTo() {
+ node_bounds = d3.selectAll("svg.graph").node().getBBox();
+ svg_bounds = d3.select("rect").node().getBBox();
+ //console.log(node_bounds, svg_bounds)
+
+ //var diff_x = Math.abs(node_bounds.x)+Math.abs(node_bounds.width);
+ perc_x = width/(node_bounds.width+100);
+
+ //var diff_y = Math.abs(node_bounds.y)+Math.abs(node_bounds.height);
+ perc_y = height/(node_bounds.height+100);
+ perc = d3.min([perc_x, perc_y])
+ //console.log(perc_x, perc)
+ d3.select('svg')
+ .transition()
+ .call(zoom.scaleBy, perc);
+}
+
+/*
+function zoomTo() {
+ var bounds = root.node().getBBox();
+ //var bounds = d3.select(".node").node().getBBox();
+ var parent = root.node().parentElement;
+ var fullWidth = parent.clientWidth,
+ fullHeight = parent.clientHeight;
+ var width = bounds.width,
+ height = bounds.height;
+ var midX = bounds.x + width / 2,
+ midY = bounds.y + height / 2;
+ if (width == 0 || height == 0) return; // nothing to fit
+ var scale = (0.75) / Math.max(width / fullWidth, height / fullHeight);
+ var translate = [fullWidth / 2 - scale * midX, fullHeight / 2 - scale * midY];
+
+ console.trace("zoomFit", translate, scale);
+ root
+ .transition()
+ .call(zoom.translate(translate).scale(scale).event);
+}
+*/
+/*function zoomTo() {
+ x_array = [];
+ y_array = [];
+ d3.selectAll(".node").each(function(d) {
+ //ctm = d[0][0].getCTM();
+ //xy_trans = d3.translate(d.x, d.y);
+ //x_array.push(xy_trans[0]);
+ // x_array.push(ctm.e + d.x*ctm.a + d.y*ctm.c);
+ x_array.push(d.x);
+ y_array.push(d.y)
+ console.log(d.x, d.y)
+
+ })
+
+ var max_x = d3.max(x_array);
+ var min_x = d3.min(x_array);
+ var diff_x = max_x-min_x-50;
+ perc_y = (diff_x*13)/width;
+ //if (perc_y < 1) {perc_y = perc_y+1;}
+
+ var max_y = d3.max(y_array);
+ var min_y = d3.min(y_array);
+ var diff_y = max_y-min_y-50;
+ perc_x = (diff_y*13)/height;
+ //if (perc_x < 1) {perc_x = perc_y+1;}
+
+ console.log(max_y, min_y)
+
+ perc = d3.max([perc_x, perc_y])
+ console.log(perc_x, perc)
+ d3.select('svg')
+ .transition()
+ .call(zoom.scaleBy, perc);
+}*/
+
/**
* initializes and shows links
* @param {object} links - links
@@ -173,6 +251,8 @@ function updateNodes(nodes) {
.attr("class", "node")
.attr("initial_x", function(d) {return d.dx;})
.attr("initial_y", function(d) {return d.dy;})
+ //.attr("abs_x", function(d) {return parseInt(d.attr("cx")) + d[0][0].getCTM().e})
+ //.attr("abs_y", function(d) {return parseInt(d.attr("cy")) + d[0][0].getCTM().f})
.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
@@ -188,7 +268,8 @@ function updateNodes(nodes) {
.attr("class", "text")
.style("font-size", "15px")
.style('pointer-events', 'auto')
- .text(function (d) {return firstauthor(d.author);})
+ .text(function (d) {const firstauthor=d.author[0].split(" ")
+ return firstauthor[firstauthor.length-1];})
.on('click', clickNode);
}
@@ -220,6 +301,7 @@ function updateMarker(color, target) {
* @param {object} node - node
*/
function clickNode(node) {
+ fix_nodes(node);
if(toRemove){
d3.select(toRemove).selectAll(".circle").style("stroke","none")
}
@@ -253,10 +335,7 @@ function create_author_array(authors){
}
function self_cit(source,target){
- sourceauthors = create_author_array(source.author)
- targetauthors = create_author_array(target.author)
-
- return sourceauthors.some(item=>targetauthors.includes(item))
+ return source.author.some(item=>target.author.includes(item))
}
/**
@@ -281,19 +360,7 @@ function isLinkForNode(node, link){
return link.source.index == node.index || link.target.index == node.index;
}
-/**
-* returns last name of first author
-* @param {string} authors - the comma-separated string of authors
-*/
-function firstauthor(authors){
- if (/,/.test(authors)==false){
- var firstauthor=/^.*\s+([\w\-]+)[\.\s]*$/.exec(authors)
- }
- else {
- var firstauthor=/^[\s\w\.\-]*\s([\w\-]+)[\.\s]*,.*$/.exec(authors)
- }
- return firstauthor[1]
-}
+
/**
* outputs node info to textbox
@@ -301,7 +368,7 @@ function firstauthor(authors){
*/
function textfunc(node){
textinfo="Title:" + '</br>' + node.name +
- '</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Year:"+'</br>'
+ '</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
+node.year+'</br>'+'</br>'+"doi:"+'</br>'+'<a href="'+node.doi+ '">'+node.doi
+'</a>'+'</br>'+'</br>'+"Citations:"+'</br>'+node.citations;
textabstract=node.abstract;
@@ -361,8 +428,18 @@ function dragstarted(node) {
function dragged(node) {
node.fx = d3.event.x;
node.fy = d3.event.y;
+ fix_nodes(node);
}
+function fix_nodes(this_node) {
+ node.each(function(d) {
+ if (this_node != d) {
+ d.fx = d.x;
+ d.fy = d.y;
+ }
+ });
+ }
+
/**
* resets the positions of the nodes
*/
diff --git a/Output/Graph/json_text.json b/Output/Graph/json_text.json
index 2ac1c17..dff9328 100644
--- a/Output/Graph/json_text.json
+++ b/Output/Graph/json_text.json
@@ -1,145 +1,437 @@
{
"nodes": [
{
- "name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis",
- "author":"Emanuel S. R. Ehmki,Robert Schmidt, Farina Ohm, Matthias Rarey",
- "year":"1997",
- "doi": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings",
+ "author": [
+ "Jerome Eberhardt",
+ "Diogo Santos-Martins",
+ "Andreas F. Tillack",
+ "Stefano Forli"
+ ],
+ "year": "July 19, 2021",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.1c00203",
"group": "input",
- "citations": 0,
- "abstract":"Ehmki ein langer text"
+ "citations":20
},
{
- "name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems ",
- "author": "John A. Keith, Valentin Vassilev-Galindo, Bingqing Cheng, Stefan Chmiela, Michael Gastegger, Klaus-Robert M\u00fcller, Alexandre Tkatchenko ",
- "year":"1937",
- "doi": "https://doi.org/10.1021/acs.chemrev.1c00107",
- "group": "citing",
- "citations": 140,
- "abstract":"Keit ein langer text"
+ "name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search",
+ "author": [
+ "Diogo Santos-Martins",
+ "Leonardo Solis-Vasquez",
+ "Andreas F Tillack",
+ "Michel F Sanner",
+ "Andreas Koch",
+ "Stefano Forli"
+ ],
+ "year": "January 6, 2021",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "group": "depth",
+ "citations":21
},
{
- "name": "Disconnected Maximum Common Substructures under Constraints ",
- "author": "Robert Schmidt, Florian Krull, Anna Lina Heinzke,Emanuel S. R. Ehmki, Matthias Rarey ",
- "year":"1991",
- "doi": "https://doi.org/10.1021/acs.jcim.0c00741",
- "group": "citing",
- "citations": 300,
- "abstract":"Schmidt ein langer text"
+ "name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep",
+ "author": [
+ "Yuqi Zhang",
+ "Michel F. Sanner"
+ ],
+ "year": "September 11, 2019",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.9b00557",
+ "group": "depth",
+ "citations":40
},
{
- "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":"2001",
- "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332",
- "group": "input",
- "citations": 250,
- "abstract":"Schuffenhauer ein langer text"
- },
- {
- "name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms ",
- "author": "Robert Schmidt, Emanuel S. R. Ehmki, Farina Ohm, Hans-Christian Ehrlich, Andriy Mashychev, Matthias Rarey ",
- "year":"2021",
- "doi": "https://doi.org/10.1021/acs.jcim.9b00250",
- "group": "cited",
- "citations": 130,
- "abstract":"Schmidt ein langer text"
- },
- {
- "name": "Machine learning accelerates quantum mechanics predictions of molecular crystals ",
- "author": "Yanqiang Han, Imran Ali, Zhilong Wang, Junfei Cai, Sicheng Wu, Jiequn Tang, Lin Zhang, Jiahao Ren, Rui Xiao, Qianqian Lu, Lei Hang, Hongyuan Luo, Jinjin Li ",
- "year":"2011",
- "doi": "https://doi.org/10.1016/j.physrep.2021.08.002",
- "group": "cited",
- "citations": 170,
- "abstract":"Han ein langer text"
- },
- {
- "name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID ",
- "author": "Ilaria Proietti Silvestri, Robert Schmidt,Nadine Schneider ,Paul J. J. Colbon ",
- "year":"2001",
- "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251",
- "group": "cited",
- "citations": 210,
- "abstract":"Silvestri ein langer text"
- },
- {
- "name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies ",
- "author": "Paul D. Leeson,Ansgar Schuffenhauer, A. Patricia Bento, Anna Gaulton, Anne Hersey, Emma J. Manners, Chris J. Radoux, Andrew R. Leach ",
- "year":"2003",
- "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416",
- "group": "cited",
- "citations": 10,
- "abstract":"Leeson ein langer text"
- },
- {
- "name": "BonMOLi\u00e8re: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space ",
- "author": "Neann Mathai, Conrad Stork, Johannes Kirchmair ",
- "year":"2003",
- "doi": "https://doi.org/10.3390/ijms22157773",
- "group": "cited",
- "citations": 80,
- "abstract":"Mathai ein langer text"
- },
- {
- "name": "Accelerating high-throughput virtual screening through molecular pool-based active learning ",
- "author": "David E. Graff, Eugene I. Shakhnovich, Connor W. Coley ",
- "year":"2013",
- "doi": "https://doi.org/10.1039/D0SC06805E",
- "group": "cited",
- "citations": 60,
- "abstract":"Graff ein langer text"
- },
- {
- "name": "Compound Screening ",
- "author": "Shin Numao",
- "year":"2009",
- "doi": "https://doi.org/10.1016/B978-0-12-820472-6.00078-5",
- "group": "citing",
- "citations": 280,
- "abstract":"Numao ein langer text"
+ "name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise",
+ "author": [
+ "David Ryan Koes",
+ "Matthew P. Baumgartner",
+ "Carlos J. Camacho"
+ ],
+ "year": "February 4, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300604z",
+ "group": "depth",
+ "citations":80
+ },
+ {
+ "name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking",
+ "author": [
+ "Anita K. Nivedha",
+ "David F. Thieker",
+ "Spandana Makeneni",
+ "Huimin Hu",
+ "Andreas F Tillack",
+ "Robert J. Woods"
+ ],
+ "year": "January 8, 2016",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.5b00834",
+ "group": "depth",
+ "citations":100
+ },
+ {
+ "name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems",
+ "author": [
+ "Stefano Forli",
+ "Maurizio Botta"
+ ],
+ "year": "June 22, 2007",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci700036j",
+ "group": "depth",
+ "citations":150
+ },
+ {
+ "name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins",
+ "author": [
+ "Diogo Santos-Martins",
+ "Stefano Forli",
+ "Maria Jo\u00e3o Ramos",
+ "Arthur J. Olson"
+ ],
+ "year": "June 15, 2014",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci500209e",
+ "group": "depth",
+ "citations":100
+ },
+ {
+ "name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking",
+ "author": [
+ "Stefano Forli",
+ "Arthur J. Olson"
+ ],
+ "year": "December 9, 2011",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm2005145",
+ "group": "depth",
+ "citations":200
+ },
+ {
+ "name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context",
+ "author": [
+ "Douglas R. Houston",
+ "Malcolm D. Walkinshaw"
+ ],
+ "year": "January 27, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300399w",
+ "group": "depth",
+ "citations":200
+ },
+ {
+ "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory",
+ "author": [
+ "Themis Lazaridis"
+ ],
+ "year": "April 14, 1998",
+ "journal": "Journal of Physical Chemistry B",
+ "doi": "https://doi.org/10.1021/jp9723574",
+ "group": "depth",
+ "citations":80
+ },
+ {
+ "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids",
+ "author": [
+ "Themis Lazaridis",
+ "Andreas F Tillack"
+ ],
+ "year": "April 14, 1998",
+ "journal": "Journal of Physical Chemistry B",
+ "doi": "https://doi.org/10.1021/jp972358w",
+ "group": "depth",
+ "citations":110
+ },
+ {
+ "name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery",
+ "author": [
+ "John J. Irwin",
+ "Khanh G. Tang",
+ "Jennifer Young",
+ "Chinzorig Dandarchuluun",
+ "Benjamin R. Wong",
+ "Munkhzul Khurelbaatar",
+ "Yurii S. Moroz",
+ "John Mayfield",
+ "Roger A. Sayle"
+ ],
+ "year": "October 29, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.0c00675",
+ "group": "depth",
+ "citations":270
+ },
+ {
+ "name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors",
+ "author": [
+ "Yan Jiang",
+ "Chunlin Zhuang",
+ "Long Chen",
+ "Junjie Lu",
+ "Guoqiang Dong",
+ "Zhenyuan Miao",
+ "Wannian Zhang",
+ "Jian Li",
+ "Chunquan Sheng"
+ ],
+ "year": "September 20, 2017",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/acs.jmedchem.7b01243",
+ "group": "depth",
+ "citations":70
+ },
+ {
+ "name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking",
+ "author": [
+ "Michael M. Mysinger",
+ "Michael Carchia",
+ "John. J. Irwin",
+ "Brian K. Shoichet"
+ ],
+ "year": "June 20, 2012",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm300687e",
+ "group": "depth",
+ "citations":400
+ },
+ {
+ "name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark",
+ "author": [
+ "Thomas Gaillard"
+ ],
+ "year": "July 10, 2018",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.8b00312",
+ "group": "depth",
+ "citations":310
+ },
+ {
+ "name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity",
+ "author": [
+ "Nguyen Thanh Nguyen",
+ "Trung Hai Nguyen",
+ "T. Ngoc Han Pham",
+ "Nguyen Truong Huy",
+ "Mai Van Bay",
+ "Minh Quan Pham",
+ "Pham Cam Nam",
+ "Van V. Vu",
+ "Son Tung Ngo"
+ ],
+ "year": "December 30, 2019",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.9b00778",
+ "group": "depth",
+ "citations":170
+ },
+ {
+ "name": "Glide:\u2009 A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy",
+ "author": [
+ "Richard A. Friesner",
+ "Jay L. Banks",
+ "Robert B. Murphy",
+ "Thomas A. Halgren",
+ "Jasna J. Klicic",
+ "Daniel T. Mainz",
+ "Matthew P. Repasky",
+ "Eric H. Knoll",
+ "Mee Shelley",
+ "Jason K. Perry",
+ "David E. Shaw",
+ "Perry Francis",
+ "Peter S. Shenkin"
+ ],
+ "year": "February 27, 2004",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm0306430",
+ "group": "depth",
+ "citations":130
+ },
+ {
+ "name": "Surflex:\u2009 Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine",
+ "author": [
+ "Ajay N. Jain"
+ ],
+ "year": "January 21, 2003",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm020406h",
+ "group": "depth",
+ "citations":86
+ },
+ {
+ "name": "ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein\u2013Ligand Interactions",
+ "author": [
+ "Guo-Bo Li",
+ "Ling-Ling Yang",
+ "Wen-Jing Wang",
+ "Lin-Li Li",
+ "Sheng-Yong Yang"
+ ],
+ "year": "February 9, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300493w",
+ "group": "depth",
+ "citations":20
+ },
+ {
+ "name": "A Knowledge-Based Energy Function for Protein\u2212Ligand, Protein\u2212Protein, and Protein\u2212DNA Complexes",
+ "author": [
+ "Chi Zhang",
+ "Song Liu",
+ "Qianqian Zhu",
+ "Yaoqi Zhou"
+ ],
+ "year": "February 16, 2005",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm049314d",
+ "group": "depth",
+ "citations":39
+ },
+ {
+ "name": "Novel Anti-Hepatitis B Virus Activity of Euphorbia schimperi and Its Quercetin and Kaempferol Derivatives",
+ "author": [
+ "Mohammad K. Parvez",
+ "Sarfaraz Ahmed",
+ "Mohammed S. Al-Dosari",
+ "Mazin A. S. Abdelwahid",
+ "Ahmed H. Arbab",
+ "Stefano Forli",
+ "Adnan J. Al-Rehaily",
+ "Mai M. Al-Oqail"
+ ],
+ "year": "October 21, 2021",
+ "journal": "ACS Omega",
+ "doi": "https://doi.org/10.1021/acsomega.1c04320",
+ "group": "height",
+ "citations":180
}
],
"links": [
{
- "source": "https://doi.org/10.1021/acs.jcim.9b00249",
- "target": "https://doi.org/10.1021/acs.chemrev.1c00107"
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
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+ "name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep",
+ "author": [
+ "Yuqi Zhang",
+ "Michel F. Sanner"
+ ],
+ "year": "September 11, 2019",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.9b00557",
+ "group": "depth",
+ "citations":40
+ },
+ {
+ "name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise",
+ "author": [
+ "David Ryan Koes",
+ "Matthew P. Baumgartner",
+ "Carlos J. Camacho"
+ ],
+ "year": "February 4, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300604z",
+ "group": "depth",
+ "citations":80
+ },
+ {
+ "name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking",
+ "author": [
+ "Anita K. Nivedha",
+ "David F. Thieker",
+ "Spandana Makeneni",
+ "Huimin Hu",
+ "Andreas F Tillack",
+ "Robert J. Woods"
+ ],
+ "year": "January 8, 2016",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.5b00834",
+ "group": "depth",
+ "citations":100
+ },
+ {
+ "name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems",
+ "author": [
+ "Stefano Forli",
+ "Maurizio Botta"
+ ],
+ "year": "June 22, 2007",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci700036j",
+ "group": "depth",
+ "citations":150
+ },
+ {
+ "name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins",
+ "author": [
+ "Diogo Santos-Martins",
+ "Stefano Forli",
+ "Maria Jo\u00e3o Ramos",
+ "Arthur J. Olson"
+ ],
+ "year": "June 15, 2014",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci500209e",
+ "group": "depth",
+ "citations":100
+ },
+ {
+ "name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking",
+ "author": [
+ "Stefano Forli",
+ "Arthur J. Olson"
+ ],
+ "year": "December 9, 2011",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm2005145",
+ "group": "depth",
+ "citations":200
+ },
+ {
+ "name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context",
+ "author": [
+ "Douglas R. Houston",
+ "Malcolm D. Walkinshaw"
+ ],
+ "year": "January 27, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300399w",
+ "group": "depth",
+ "citations":200
+ },
+ {
+ "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory",
+ "author": [
+ "Themis Lazaridis"
+ ],
+ "year": "April 14, 1998",
+ "journal": "Journal of Physical Chemistry B",
+ "doi": "https://doi.org/10.1021/jp9723574",
+ "group": "depth",
+ "citations":80
+ },
+ {
+ "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids",
+ "author": [
+ "Themis Lazaridis",
+ "Andreas F Tillack"
+ ],
+ "year": "April 14, 1998",
+ "journal": "Journal of Physical Chemistry B",
+ "doi": "https://doi.org/10.1021/jp972358w",
+ "group": "depth",
+ "citations":110
+ },
+ {
+ "name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery",
+ "author": [
+ "John J. Irwin",
+ "Khanh G. Tang",
+ "Jennifer Young",
+ "Chinzorig Dandarchuluun",
+ "Benjamin R. Wong",
+ "Munkhzul Khurelbaatar",
+ "Yurii S. Moroz",
+ "John Mayfield",
+ "Roger A. Sayle"
+ ],
+ "year": "October 29, 2020",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.0c00675",
+ "group": "depth",
+ "citations":270
+ },
+ {
+ "name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors",
+ "author": [
+ "Yan Jiang",
+ "Chunlin Zhuang",
+ "Long Chen",
+ "Junjie Lu",
+ "Guoqiang Dong",
+ "Zhenyuan Miao",
+ "Wannian Zhang",
+ "Jian Li",
+ "Chunquan Sheng"
+ ],
+ "year": "September 20, 2017",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/acs.jmedchem.7b01243",
+ "group": "depth",
+ "citations":70
+ },
+ {
+ "name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking",
+ "author": [
+ "Michael M. Mysinger",
+ "Michael Carchia",
+ "John. J. Irwin",
+ "Brian K. Shoichet"
+ ],
+ "year": "June 20, 2012",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm300687e",
+ "group": "depth",
+ "citations":400
+ },
+ {
+ "name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark",
+ "author": [
+ "Thomas Gaillard"
+ ],
+ "year": "July 10, 2018",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.8b00312",
+ "group": "depth",
+ "citations":310
+ },
+ {
+ "name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity",
+ "author": [
+ "Nguyen Thanh Nguyen",
+ "Trung Hai Nguyen",
+ "T. Ngoc Han Pham",
+ "Nguyen Truong Huy",
+ "Mai Van Bay",
+ "Minh Quan Pham",
+ "Pham Cam Nam",
+ "Van V. Vu",
+ "Son Tung Ngo"
+ ],
+ "year": "December 30, 2019",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.9b00778",
+ "group": "depth",
+ "citations":170
+ },
+ {
+ "name": "Glide:\u2009 A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy",
+ "author": [
+ "Richard A. Friesner",
+ "Jay L. Banks",
+ "Robert B. Murphy",
+ "Thomas A. Halgren",
+ "Jasna J. Klicic",
+ "Daniel T. Mainz",
+ "Matthew P. Repasky",
+ "Eric H. Knoll",
+ "Mee Shelley",
+ "Jason K. Perry",
+ "David E. Shaw",
+ "Perry Francis",
+ "Peter S. Shenkin"
+ ],
+ "year": "February 27, 2004",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm0306430",
+ "group": "depth",
+ "citations":130
+ },
+ {
+ "name": "Surflex:\u2009 Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine",
+ "author": [
+ "Ajay N. Jain"
+ ],
+ "year": "January 21, 2003",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm020406h",
+ "group": "depth",
+ "citations":86
+ },
+ {
+ "name": "ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein\u2013Ligand Interactions",
+ "author": [
+ "Guo-Bo Li",
+ "Ling-Ling Yang",
+ "Wen-Jing Wang",
+ "Lin-Li Li",
+ "Sheng-Yong Yang"
+ ],
+ "year": "February 9, 2013",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/ci300493w",
+ "group": "depth",
+ "citations":20
+ },
+ {
+ "name": "A Knowledge-Based Energy Function for Protein\u2212Ligand, Protein\u2212Protein, and Protein\u2212DNA Complexes",
+ "author": [
+ "Chi Zhang",
+ "Song Liu",
+ "Qianqian Zhu",
+ "Yaoqi Zhou"
+ ],
+ "year": "February 16, 2005",
+ "journal": "Journal of Medicinal Chemistry",
+ "doi": "https://doi.org/10.1021/jm049314d",
+ "group": "depth",
+ "citations":39
+ },
+ {
+ "name": "Novel Anti-Hepatitis B Virus Activity of Euphorbia schimperi and Its Quercetin and Kaempferol Derivatives",
+ "author": [
+ "Mohammad K. Parvez",
+ "Sarfaraz Ahmed",
+ "Mohammed S. Al-Dosari",
+ "Mazin A. S. Abdelwahid",
+ "Ahmed H. Arbab",
+ "Stefano Forli",
+ "Adnan J. Al-Rehaily",
+ "Mai M. Al-Oqail"
+ ],
+ "year": "October 21, 2021",
+ "journal": "ACS Omega",
+ "doi": "https://doi.org/10.1021/acsomega.1c04320",
+ "group": "height",
+ "citations":180
+ }
+ ],
+ "links": [
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jctc.0c01006"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jctc.9b00557"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci300604z"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jctc.5b00834"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci700036j"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci500209e"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jm2005145"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci300399w"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci300399w"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jp9723574"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jp972358w"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jcim.0c00675"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jmedchem.7b01243"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jm300687e"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jcim.8b00312"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/acs.jcim.9b00778"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jm0306430"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jm020406h"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/ci300493w"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.1c00203",
+ "target": "https://doi.org/10.1021/jm049314d"
+ },
+ {
+ "source": "https://doi.org/10.1021/acsomega.1c04320",
+ "target": "https://doi.org/10.1021/acs.jcim.1c00203"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.8b00312",
+ "target": "https://doi.org/10.1021/ci300604z"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "target": "https://doi.org/10.1021/ci700036j"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jctc.9b00557",
+ "target": "https://doi.org/10.1021/ci700036j"
+ },
+ {
+ "source": "https://doi.org/10.1021/ci500209e",
+ "target": "https://doi.org/10.1021/ci700036j"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "target": "https://doi.org/10.1021/ci500209e"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "target": "https://doi.org/10.1021/jm2005145"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.8b00312",
+ "target": "https://doi.org/10.1021/jm2005145"
+ },
+ {
+ "source": "https://doi.org/10.1021/ci500209e",
+ "target": "https://doi.org/10.1021/jm2005145"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00778",
+ "target": "https://doi.org/10.1021/acs.jcim.8b00312"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "target": "https://doi.org/10.1021/acs.jcim.9b00778"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js b/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
index ce08a98..95d2792 100644
--- a/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
+++ b/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
@@ -24,7 +24,7 @@ color = d3.scaleOrdinal()
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
yscale = d3.scaleOrdinal()
.domain(["citing", "input", "cited"])
- .range([0, 200, 400]),
+ .range([0, 250, 500]),
linetype=d3.scaleOrdinal()
.domain(["line","dotted"])
.range([("8,0"),("8,8")]),
@@ -105,12 +105,15 @@ legendarrow.append("text")
* arranges the nodes according to their group on the y-axis
*/
var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(100).strength(1))
- .force("collide", d3.forceCollide(60))
- .force("charge", d3.forceManyBody().strength(-50))
- .force("center", d3.forceCenter(width/2, height/2+50))
- .force("xscale", d3.forceX().strength(1).x(function(d) {return xscale(parseFloat(d.year))}))
- .force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}));
+ .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(60))
+ .force("collide", d3.forceCollide(50))
+ //.force("manyBody", d3.forceManyBody())
+ .force("charge", d3.forceManyBody())
+ .force("center", d3.forceCenter(width/2, height/2))
+ //.force("xscale", d3.forceX().strength(1).x(function(d) {return xscale(parseInt(d.year))}))
+ .alpha(0.1)
+ //.alphaDecay(0)
+ //.force("yscale", d3.forceY().strength(0.5).y(function(d) {return yscale(d.group)}));
/**
* creates group element
@@ -176,9 +179,10 @@ function update(links, nodes) { //THISS
function updateXAxis(nodes) {
years = [];
for (i = 0; i < nodes.length; i++) {
- years.push(parseFloat(nodes[i]["year"]));
+ years.push(parseInt((nodes[i]["year"]).split(" ")[2]));
}
+ console.log(years)
xscale = d3.scaleLinear()
.domain([d3.min(years)-10, d3.max(years)+10])
.range([50, width-50])
@@ -214,7 +218,7 @@ function updateNodes(nodes) {
.enter()
.append("g")
.attr("class", "node")
- .attr('dx', function(d) {return xscale(parseFloat(d.year))})
+ .attr('dx', function(d) {return xscale(parseInt((d.year).split(" ")[2]))})
.attr("initial_x", function(d) {return d.dx;})
.attr("initial_y", function(d) {return d.dy;})
.call(d3.drag()
@@ -233,7 +237,10 @@ function updateNodes(nodes) {
.attr("class", "text")
.style("font-size", "15px")
.style('pointer-events', 'auto')
- .text(function (d) {return firstauthor(d.author);})
+ .text(function (d) {
+ const firstauthor = d.author[0].split(" ")
+ return firstauthor[firstauthor.length-1];
+ })
.on('click', clickNode);
}
@@ -274,6 +281,7 @@ function clickNode(node) {
textfunc(node)
resetbuttonhighlight()
highlightbutton("overview")
+ fix_nodes(node);
}
/**
@@ -285,20 +293,21 @@ function clickRect() {
.style("stroke", "#999")
.attr('marker-end', function(d) {return updateMarker('#999', d.target);})
document.getElementById('textbox').innerHTML = "Click node";
+ fix_nodes(node);
}
function create_author_array(authors){
- authorarray = authors.split(",")
- authorarray = authorarray.map(elem =>{return elem.trim();})
+ //authorarray = authors.split(",")
+ //authorarray = authorarray.map(elem =>{return elem.trim();})
- return authorarray
+ //return authorarray
}
function self_cit(source,target){
- sourceauthors = create_author_array(source.author)
- targetauthors = create_author_array(target.author)
+ //sourceauthors = create_author_array(source.author)
+ //targetauthors = create_author_array(target.author)
- return sourceauthors.some(item=>targetauthors.includes(item))
+ return source.author.some(item=>target.author.includes(item))
}
/**
* sets color of link (line and arrowhead) to black if it is directly connected to node
@@ -379,11 +388,11 @@ function displayabstract(a){
* updates the positions of the links and nodes
*/
function tickHandler() {
- link.attr("x1", function (d) {return xscale(parseInt(d.source.year));})
+ link.attr("x1", function (d) {return xscale(parseInt((d.source.year).split(" ")[2]));})
.attr("y1", function (d) {return d.source.y;})
- .attr("x2", function (d) {return xscale(parseInt(d.target.year));})
+ .attr("x2", function (d) {return xscale(parseInt((d.target.year).split(" ")[2]));})
.attr("y2", function (d) {return d.target.y;});
- node.attr("transform", function (d) {return "translate(" + xscale(parseInt(d.year)) + ", " + d.y + ")";});
+ node.attr("transform", function (d) {return "translate(" + xscale(parseInt((d.year).split(" ")[2])) + ", " + d.y + ")";});
}
/**
@@ -393,8 +402,9 @@ function tickHandler() {
function dragstarted(node) {
if (!d3.event.active)
simulation.alphaTarget(0.3).restart()
- node.fx = node.x;
+ //node.fx = node.x;
node.fy = node.y;
+ fix_nodes(node);
}
/**
@@ -402,9 +412,18 @@ function dragstarted(node) {
* @param {object} node - data of current node
*/
function dragged(node) {
- node.fx = d3.event.x;
+ // node.fx = d3.event.x;
node.fy = d3.event.y;
+ fix_nodes(node);
}
+function fix_nodes(this_node) {
+ node.each(function(d) {
+ if (this_node != d) {
+ d.fx = d.x;
+ d.fy = d.y;
+ }
+ });
+ }
/**
* ends the dragging and resets the position of the node
diff --git a/Output/Graph_mit_Zeitstrahl/json_text.json b/Output/Graph_mit_Zeitstrahl/json_text.json
index 2ac1c17..35b5f89 100644
--- a/Output/Graph_mit_Zeitstrahl/json_text.json
+++ b/Output/Graph_mit_Zeitstrahl/json_text.json
@@ -1,145 +1,437 @@
{
"nodes": [
{
- "name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis",
- "author":"Emanuel S. R. Ehmki,Robert Schmidt, Farina Ohm, Matthias Rarey",
- "year":"1997",
- "doi": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings",
+ "author": [
+ "Jerome Eberhardt",
+ "Diogo Santos-Martins",
+ "Andreas F. Tillack",
+ "Stefano Forli"
+ ],
+ "year": "July 19, 2021",
+ "journal": "Journal of Chemical Information and Modeling",
+ "doi": "https://doi.org/10.1021/acs.jcim.1c00203",
"group": "input",
- "citations": 0,
- "abstract":"Ehmki ein langer text"
+ "citations":20
},
{
- "name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems ",
- "author": "John A. Keith, Valentin Vassilev-Galindo, Bingqing Cheng, Stefan Chmiela, Michael Gastegger, Klaus-Robert M\u00fcller, Alexandre Tkatchenko ",
- "year":"1937",
- "doi": "https://doi.org/10.1021/acs.chemrev.1c00107",
- "group": "citing",
- "citations": 140,
- "abstract":"Keit ein langer text"
+ "name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search",
+ "author": [
+ "Diogo Santos-Martins",
+ "Leonardo Solis-Vasquez",
+ "Andreas F Tillack",
+ "Michel F Sanner",
+ "Andreas Koch",
+ "Stefano Forli"
+ ],
+ "year": "January 6, 2021",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.0c01006",
+ "group": "depth",
+ "citations":21
},
{
- "name": "Disconnected Maximum Common Substructures under Constraints ",
- "author": "Robert Schmidt, Florian Krull, Anna Lina Heinzke,Emanuel S. R. Ehmki, Matthias Rarey ",
- "year":"1991",
- "doi": "https://doi.org/10.1021/acs.jcim.0c00741",
- "group": "citing",
- "citations": 300,
- "abstract":"Schmidt ein langer text"
+ "name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep",
+ "author": [
+ "Yuqi Zhang",
+ "Michel F. Sanner"
+ ],
+ "year": "September 11, 2019",
+ "journal": "Journal of Chemical Theory and Computation",
+ "doi": "https://doi.org/10.1021/acs.jctc.9b00557",
+ "group": "depth",
+ "citations":40
},
{
- "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":"2001",
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- "group": "input",
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--
GitLab