-
Notifications
You must be signed in to change notification settings - Fork 0
/
grants.yaml
452 lines (409 loc) · 22.8 KB
/
grants.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
%YAML 1.2
---
# This YAML file contains information about all the grants and contracts (current and completed) that fund the Chodera lab
#
# Current grants: http://www.choderalab.org/funding
# Here is an illustrative entry for grants
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NIH R35 GM152017"
# 'title' is the title of the grant
title: "Teaching free energy calculations to learn"
# 'pi' is the lead investigator
pi: John D. Chodera
# 'role' is the role in the grant
role: PI
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Institutes of Health"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 1530000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2024-03-01
project_end_date: 2029-02-28
# URL to official grant record, if applicable
url: "https://reporter.nih.gov/search/YrAzMD62YEqc1BLw9OFeRA/project-details/10765274"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop and apply new methods that integrate physical models and machine learning to predict
free energies relevant to drug discovery, such as binding affinities.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NIH P30 CA008748"
# 'title' is the title of the grant
title: "Cancer Center Support Grant"
# 'pi' is the lead investigator
pi: Craig B. Thompson
# 'role' is the role in the grant
role: Senior/Key Personnel
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Institutes of Health"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 0
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 1997-01-20
project_end_date: 2023-12-31
# URL to official grant record, if applicable
url: "https://projectreporter.nih.gov/project_info_details.cfm?aid=10050633&icde=50797695"
# Description of the goal of the project (must be followed by two blank lines)
description: >
This grant supports Memorial Sloan Kettering Cancer Center (MSK), a free-standing NCI-designated Comprehensive Cancer
Center dedicated to improving the standards of cancer treatment, prevention and control.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NIH R01 GM121505"
# 'title' is the title of the grant
title: "Quantitative dissection of the origin of kinase inhibitor selectivity"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Institutes of Health"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 981250
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2017-09-15
project_end_date: 2022-08-31
# URL to official grant record, if applicable
url: "https://public.era.nih.gov/grantfolder/piAppDetails/genericStatus.do?encryptedParam=vglppgLq-x8.uktQknguXWR0u0of-5pOGLUIYcZhKRWcSBKVmGbuGyU."
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to characterize the role of conformational reorganization energetics in achieving
targeted kinase inhibitor selectivity.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NIH R01 GM124270"
# 'title' is the title of the grant
title: "The goal of this project is to enable blind community challenges that drive progress toward quantitative accuracy in the field of computational physical modeling of drug-receptor interactions."
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Institutes of Health"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 230352
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2018-09-10
project_end_date: 2022-08-31
# URL to official grant record, if applicable
url: "https://projectreporter.nih.gov/project_info_description.cfm?aid=9521419&icde=41560906&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC&pball="
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to enable blind community challenges that drive progress toward quantitative
accuracy in the field of computational physical modeling of drug-receptor interactions.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Relay Therapeutics Collaboration"
# 'title' is the title of the grant
title: "Development of efficient open source cloud-enabled free energy based lead optimization algorithms and integrative Bayesian model of experimental biophysical and molecular simulation data"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Relay Therapeutics"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 124828
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2018-04-05
project_end_date: 2022-04-05
# URL to official grant record, if applicable
url: "https://relaytx.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop open source scalable cloud workflows for lead optimization using
relative and absolute alchemical free energy calculations, as well as Bayesian integrative modeling
techniques for experimental biophysical data and molecular simulations.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Entasis Therapeutics Collaboration"
# 'title' is the title of the grant
title: "Development of efficient equilibrium and nonequilibrium algorithms for predicting small molecule porin permeation with potential of mean force methods"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Entasis Therapeutics"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 74074
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2018-04-05
project_end_date: 2019-04-05
# URL to official grant record, if applicable
url: "http://www.entasistx.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop algorithms and open source tools for efficient equilibrium and
nonequilibrium potential of mean force calculations for bacterial porins.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Vir Biotechnology Collaboration"
# 'title' is the title of the grant
title: "Predicting resistance vulnerabilities of an ultra-potent RSV antibody"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Vir Biotechnology"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 166668
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2019-08-01
project_end_date: 2022-07-31
# URL to official grant record, if applicable
url: "https://www.vir.bio/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop alchemical free energy methods for predicting the impact of
point mutations on antibody:antigen affinities.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Bayer Collaboration"
# 'title' is the title of the grant
title: "Development of a combined machine learning / alchemical free energy approach to predict the impact of mutations on small molecule kinase inhibitor binding"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Bayer"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 117105
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2020-03-01
project_end_date: 2022-04-30
# URL to official grant record, if applicable
url: "https://www.bayer.com"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop open source scalable free energy and machine learning workflows to predict
which mutations of kinases small molecule therapeutics may be effective against.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Interline Therapeutics Collaboration"
# 'title' is the title of the grant
title: "Developing predictive modeling techniques for modulating protein-protein interactions with small molecules"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Interline Therapeutics"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 495427
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2019-07-25
project_end_date: 2021-07-24
# URL to official grant record, if applicable
url: "https://www.foresitelabs.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop predictive models for modulating protein-protein interactions with small molecules.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Parker Institute for Cancer Immunotherapy Pilot Grant"
# 'title' is the title of the grant
title: "Physics-based computational prediction of cancer-associated mutant MHC class II epitopes"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Parker Institute for Cancer Immunotherapy"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 75000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2018-04-02
project_end_date: 2019-04-01
# URL to official grant record, if applicable
url: "https://www.parkerici.org/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
None
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "MSKCC Functional Genomics Initiative"
# 'title' is the title of the grant
title: "Integrated approaches annotate functions of cancer-associated H3K36 methyltransferases"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "MSKCC"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 125000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2018-12-01
project_end_date: 2020-11-30
# URL to official grant record, if applicable
url: "https://www.mskcc.org"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to use a combined experimental-computational approach to annotate the
functional impact of clinical cancer mutations in H3K36 methyltransferases
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Einstein BIH Visiting Fellowship"
# 'title' is the title of the grant
title: "Computational polypharmacology: A new paradigm for selectively promiscuous kinase inhibitors"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Stiftung Charité - Einstein Foundation"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: EUR 150000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2019-02-01
project_end_date: 2022-01-31
# URL to official grant record, if applicable
url: "https://www.stiftung-charite.de/funding/the-private-excellence-initiative-johanna-quandt/?L=1"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop open source tools for integrating structure-informed machine
learning and alchemical free energy calculations for the design of selectively promiscuous kinase inhibitors.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NIH P30CA008748"
# 'title' is the title of the grant
title: "MSKCC Cancer Center Grant"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Institutes of Health"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs:
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin:
project_end_date:
# URL to official grant record, if applicable
url: "http://www.nih.gov/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
None
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "XtalPi Open Force Field Consortium"
# 'title' is the title of the grant
title: "Distinguished Postdoctoral Fellowship"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "XtalPi "
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs:
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin:
project_end_date:
# URL to official grant record, if applicable
url: "http://www.xtalpi.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
None
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Open Force Field Consortium"
# 'title' is the title of the grant
title: "Open Force Field Consortium"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Open Force Field"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs:
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin:
project_end_date:
# URL to official grant record, if applicable
url: "https://openforcefield.org/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The Open Force Field Consortium is composed of academic investigators from the Open Force Field
Initiative and sponsoring Industry Partners collaborating to advance open force field science,
toolkits, and standards for biomolecular drug discovery.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "NSF CHE-1738979"
# 'title' is the title of the grant
title: "NSF Data-Driven Discovery Science in Chemistry (D3SC)"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: federal
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "National Science Foundation"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 104113
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2017-08-01
project_end_date: 2019-07-31
# URL to official grant record, if applicable
url: "https://nsf.gov/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this proposal is to explore Bayesian approaches to determining forcefield parameters from
experimental data and propagating uncertainty in predictions.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Merck KGaA Collaboration"
# 'title' is the title of the grant
title: "Developing automated workflows for absolute alchemical free energy calculations with YANK"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Merck KGaA"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 387176
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2016-07-26
project_end_date: 2019-01-25
# URL to official grant record, if applicable
url: "https://www.emdgroup.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to develop automated workflows for absolute alchemical free energy
calculations with YANK, an open source code developed in the lab.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Silicon Therapeutics Collaboration"
# 'title' is the title of the grant
title: "Development of efficient open source free energy-based lead optimization algorithms"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Silicon Therapeutics"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 84076
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2017-05-17
project_end_date: 2018-11-17
# URL to official grant record, if applicable
url: "http://www.silicontx.com/"
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to compare the performance of single-replica and nonequilibrium
alchemical free energy methods for relative free energy calculations.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Starr Foundation Grant I8-A8-058"
# 'title' is the title of the grant
title: "Designing sinefungin scaffolds as specific protein methyltransferase inhibitors"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Starr Foundation"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 125000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2015-01-01
project_end_date: 2017-06-30
# URL to official grant record, if applicable
url: " "
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to design selective inhibitors for protein lysine methyltransferases
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Astra-Zeneca iMED Collaboration"
# 'title' is the title of the grant
title: "Evaluating the potential for Markov state models of conformational dynamics to advance quantitative prediction of thermodynamics and kinetics of selective kinase inhibitors"
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: industry
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Astra-Zeneca iMED "
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 176258
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2015-07-30
project_end_date: 2017-01-30
# URL to official grant record, if applicable
url: " "
# Description of the goal of the project (must be followed by two blank lines)
description: >
The goal of this project is to evaluate the potential for Markov state models of conformational dynamics
to quantitatively predict the thermodynamics and kinetics of selective kinase inhibitors to CK2 and SYK.
# 'id' is the unique identifier by which the grant is referred to in the publications YAML
- id: "Louis V Gerstner Young Investigators Award "
# 'title' is the title of the grant
title: "Young Investigators Award "
# 'type' denotes 'federal', 'industry', 'philanthropy'
type: philanthropy
# 'organization' denotes the organization (federal, industrial, or philanthropic) granting the funds
organization: "Louis V Gerstner"
# 'direct_costs' denotes the total direct cost in dollars to the lab
direct_costs: 75000
# project start and end dates in ISO 8601 format (YYYY-MM-DD)
project_begin: 2013-02-01
project_end_date: 2016-01-31
# URL to official grant record, if applicable
url: " "
# Description of the goal of the project (must be followed by two blank lines)
description: >
None