forked from barbagroup/bibtex
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathmulti_model.bib
More file actions
541 lines (488 loc) · 18.5 KB
/
multi_model.bib
File metadata and controls
541 lines (488 loc) · 18.5 KB
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
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
@article{amaro2009characterizing,
title={Characterizing loop dynamics and ligand recognition in human-and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations},
author={Amaro, Rommie E and Cheng, Xiaolin and Ivanov, Ivaylo and Xu, Dong and McCammon, J Andrew},
journal={Journal of the American Chemical Society},
volume={131},
number={13},
pages={4702--4709},
year={2009},
publisher={ACS Publications}
}
@article{plewczynski2011can,
title={Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database},
author={Plewczynski, Dariusz and {\L}a{\'z}niewski, Micha{\l} and Augustyniak, Rafa{\l} and Ginalski, Krzysztof},
journal={Journal of computational chemistry},
volume={32},
number={4},
pages={742--755},
year={2011},
publisher={Wiley Online Library}
}
@article{miller2012mmpbsa,
title={MMPBSA. py: an efficient program for end-state free energy calculations},
author={Miller III, Bill R and McGee Jr, T Dwight and Swails, Jason M and Homeyer, Nadine and Gohlke, Holger and Roitberg, Adrian E},
journal={Journal of chemical theory and computation},
volume={8},
number={9},
pages={3314--3321},
year={2012},
publisher={ACS Publications}
}
@article{OnufrievCase2019,
title={Generalized Born implicit solvent models for biomolecules},
author={Onufriev, Alexey V and Case, David A},
journal={Annual review of biophysics},
volume={48},
pages={275},
year={2019},
publisher={NIH Public Access}
}
@article{WangETal2018,
title={Recent developments and applications of the MMPBSA method},
author={Wang, Changhao and Greene, D'Artagnan and Xiao, Li and Qi, Ruxi and Luo, Ray},
journal={Frontiers in molecular biosciences},
volume={4},
pages={87},
year={2018},
publisher={Frontiers Media SA}
}
@article{LippariniMennucci2021,
title={Hybrid QM/classical models: Methodological advances and new applications},
author={Lipparini, Filippo and Mennucci, Benedetta},
journal={Chemical Physics Reviews},
volume={2},
number={4},
pages={041303},
year={2021},
publisher={AIP Publishing LLC}
}
@article{WarshelLevitt1976,
title={Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme},
author={Warshel, Arieh and Levitt, Michael},
journal={Journal of molecular biology},
volume={103},
number={2},
pages={227--249},
year={1976},
publisher={Elsevier}
}
@article{HayikETal2008,
title={A Combined QM/MM Poisson- Boltzmann Approach},
author={Hayik, Seth A and Liao, Ning and Merz Jr, Kenneth M},
journal={Journal of Chemical Theory and Computation},
volume={4},
number={8},
pages={1200--1207},
year={2008},
publisher={ACS Publications}
}
@article{kumari2014g_mmpbsa,
title={g\_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations},
author={Kumari, Rashmi and Kumar, Rajendra and Open Source Drug Discovery Consortium and Lynn, Andrew},
journal={Journal of chemical information and modeling},
volume={54},
number={7},
pages={1951--1962},
year={2014},
publisher={ACS Publications}
}
@article{kratz2016lichem,
title={LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields},
author={Kratz, Eric G and Walker, Alice R and Lagard{\`e}re, Louis and Lipparini, Filippo and Piquemal, Jean-Philip and Andr{\'e}s Cisneros, G},
journal={Journal of computational chemistry},
volume={37},
number={11},
pages={1019--1029},
year={2016},
publisher={Wiley Online Library}
}
@article{gokcan2019lichem,
title={LICHEM 1.1: recent improvements and new capabilities},
author={Gökcan, Hatice and V{\'a}zquez-Montelongo, Erik Antonio and Cisneros, G Andr{\'e}s},
journal={Journal of chemical theory and computation},
volume={15},
number={5},
pages={3056--3065},
year={2019},
publisher={ACS Publications}
}
@article{berendsen1995gromacs,
title={GROMACS: A message-passing parallel molecular dynamics implementation},
author={Berendsen, Herman JC and van der Spoel, David and van Drunen, Rudi},
journal={Computer physics communications},
volume={91},
number={1-3},
pages={43--56},
year={1995},
publisher={Elsevier}
}
@article{ponder2004tinker,
title={TINKER: Software tools for molecular design},
author={Ponder, Jay W and others},
journal={Washington University School of Medicine, Saint Louis, MO},
volume={3},
year={2004}
}
@article{turney2012psi4,
title={Psi4: an open-source ab initio electronic structure program},
author={Turney, Justin M and Simmonett, Andrew C and Parrish, Robert M and Hohenstein, Edward G and Evangelista, Francesco A and Fermann, Justin T and Mintz, Benjamin J and Burns, Lori A and Wilke, Jeremiah J and Abrams, Micah L and others},
journal={Wiley Interdisciplinary Reviews: Computational Molecular Science},
volume={2},
number={4},
pages={556--565},
year={2012},
publisher={Wiley Online Library}
}
@article{grossfield2021loos,
title={Loos, a better tool to analyze molecular dynamics simulations},
author={Grossfield, Alan and Romo, Tod D},
journal={Biophysical Journal},
volume={120},
number={3},
pages={178a},
year={2021},
publisher={Elsevier}
}
@article{michaud2011mdanalysis,
title={MDAnalysis: a toolkit for the analysis of molecular dynamics simulations},
author={Michaud-Agrawal, Naveen and Denning, Elizabeth J and Woolf, Thomas B and Beckstein, Oliver},
journal={Journal of computational chemistry},
volume={32},
number={10},
pages={2319--2327},
year={2011},
publisher={Wiley Online Library}
}
@article{eastman2010openmm,
title={OpenMM: A hardware-independent framework for molecular simulations},
author={Eastman, Peter and Pande, Vijay},
journal={Computing in science \& engineering},
volume={12},
number={4},
pages={34--39},
year={2010},
publisher={IEEE}
}
@article{zhao2022pyresp,
title={PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields},
author={Zhao, Shiji and Wei, Haixin and Cieplak, Piotr and Duan, Yong and Luo, Ray},
journal={Journal of Chemical Theory and Computation},
year={2022},
publisher={ACS Publications}
}
@article{graham2017pycgtool,
title={PyCGTOOL: automated generation of coarse-grained molecular dynamics models from atomistic trajectories},
author={Graham, James A and Essex, Jonathan W and Khalid, Syma},
journal={Journal of chemical information and modeling},
volume={57},
number={4},
pages={650--656},
year={2017},
publisher={ACS Publications}
}
@article{betcke2021bempp,
title={Bempp-cl: A fast Python based just-in-time compiling boundary element library.},
author={Betcke, Timo and Scroggs, Matthew W},
journal={Journal of Open Source Software},
volume={6},
number={59},
pages={2879},
year={2021}
}
@article{wang2021exafmm,
title={ExaFMM: a high-performance fast multipole method library with C++ and Python interfaces},
author={Wang, Tingyu and Yokota, Rio and Barba, Lorena A},
journal={Journal of Open Source Software},
volume={6},
number={61},
pages={3145},
year={2021}
}
@article{unke2021machine,
title={Machine learning force fields},
author={Unke, Oliver T and Chmiela, Stefan and Sauceda, Huziel E and Gastegger, Michael and Poltavsky, Igor and Schütt, Kristof T and Tkatchenko, Alexandre and Müller, Klaus-Robert},
journal={Chemical Reviews},
volume={121},
number={16},
pages={10142--10186},
year={2021},
publisher={ACS Publications}
}
@book{kluyver2016jupyter,
title={Jupyter Notebooks-a publishing format for reproducible computational workflows.},
author={Kluyver, Thomas and Ragan-Kelley, Benjamin and P{\'e}rez, Fernando and Granger, Brian E and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica B and Grout, Jason and Corlay, Sylvain and others},
volume={2016},
year={2016}
}
@article{mennucci1997evaluation,
title={Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: theoretical bases, computational implementation, and numerical applications},
author={Mennucci, Benedetta and Cances, E and Tomasi, Jacopo},
journal={The Journal of Physical Chemistry B},
volume={101},
number={49},
pages={10506--10517},
year={1997},
publisher={ACS Publications}
}
@article{cammi1995remarks,
title={Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: Iterative versus matrix-inversion procedures and the renormalization of the apparent charges},
author={Cammi, Roberto and Tomasi, Jacopo},
journal={Journal of computational chemistry},
volume={16},
number={12},
pages={1449--1458},
year={1995},
publisher={Wiley Online Library}
}
@article{klamt1993cosmo,
title={COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient},
author={Klamt, Andreas and Sch{\"u}{\"u}rmann, GJGJ},
journal={Journal of the Chemical Society, Perkin Transactions 2},
number={5},
pages={799--805},
year={1993},
publisher={Royal Society of Chemistry}
}
@article{gotze2021user,
title={A user-friendly, Python-based quantum mechanics/Gromacs interface: gmx2qmmm},
author={G{\"o}tze, Jan P and Pi, Yuan-Wei and Petry, Simon and Langkabel, Fabian and Witte, Jan Felix and Lemke, Oliver},
journal={International Journal of Quantum Chemistry},
volume={121},
number={3},
pages={e26486},
year={2021},
publisher={Wiley Online Library}
}
@article{rathnayake2022pyqm,
title={PyQM/MM: a Python Interface for ONIOM (QM: MM) Calculations with the AMOEBA09 Polarizable Force Field to Study the Chemical Processes in the Interstellar Medium},
author={Rathnayake, PVGM and Sameera, WMC and Watanabe, Naoki},
year={2022}
}
@article{lu2018open,
title={Open-Source, python-based redevelopment of the ChemShell multiscale QM/MM environment},
author={Lu, You and Farrow, Matthew R and Fayon, Pierre and Logsdail, Andrew J and Sokol, Alexey A and Catlow, C Richard A and Sherwood, Paul and Keal, Thomas W},
journal={Journal of chemical theory and computation},
volume={15},
number={2},
pages={1317--1328},
year={2018},
publisher={ACS Publications}
}
@article{benighaus2009general,
title={A general boundary potential for hybrid QM/MM simulations of solvated biomolecular systems},
author={Benighaus, Tobias and Thiel, Walter},
journal={Journal of Chemical Theory and Computation},
volume={5},
number={11},
pages={3114--3128},
year={2009},
publisher={ACS Publications}
}
@article{lipparini2012analytical,
title={Analytical first and second derivatives for a fully polarizable QM/classical hamiltonian},
author={Lipparini, Filippo and Cappelli, Chiara and Scalmani, Giovanni and De Mitri, Nicola and Barone, Vincenzo},
journal={Journal of Chemical Theory and Computation},
volume={8},
number={11},
pages={4270--4278},
year={2012},
publisher={ACS Publications}
}
@article{butler2018machine,
title={Machine learning for molecular and materials science},
author={Butler, Keith T and Davies, Daniel W and Cartwright, Hugh and Isayev, Olexandr and Walsh, Aron},
journal={Nature},
volume={559},
number={7715},
pages={547--555},
year={2018},
publisher={Nature Publishing Group}
}
@article{smith2017ani,
title={ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost},
author={Smith, Justin S and Isayev, Olexandr and Roitberg, Adrian E},
journal={Chemical science},
volume={8},
number={4},
pages={3192--3203},
year={2017},
publisher={Royal Society of Chemistry}
}
@article{gao2020torchani,
title={TorchANI: a free and open source PyTorch-based deep learning implementation of the ANI neural network potentials},
author={Gao, Xiang and Ramezanghorbani, Farhad and Isayev, Olexandr and Smith, Justin S and Roitberg, Adrian E},
journal={Journal of chemical information and modeling},
volume={60},
number={7},
pages={3408--3415},
year={2020},
publisher={ACS Publications}
}
@article{chmiela2017,
title={Machine Learning of Accurate Energy-conserving Molecular Force Fields},
author={Chmiela, Stefan and Tkatchenko, Alexandre and Sauceda, Huziel E. and Poltavsky, Igor and Schütt, Kristof T. and Müller, Klaus-Robert},
journal={Science Advances},
volume={3},
number={5},
pages={e1603015},
year={2017},
doi = {10.1126/sciadv.1603015}}
@article{schütt2018schnetpack,
title={SchNetPack: A deep learning toolbox for atomistic systems},
author={Schütt, KT and Kessel, Pan and Gastegger, Michael and Nicoli, KA and Tkatchenko, Alexandre and Müller, K-R},
journal={Journal of chemical theory and computation},
volume={15},
number={1},
pages={448--455},
year={2018},
publisher={ACS Publications}
}
@article{lagaris1998artificial,
title={Artificial neural networks for solving ordinary and partial differential equations},
author={Lagaris, Isaac E and Likas, Aristidis and Fotiadis, Dimitrios I},
journal={IEEE transactions on neural networks},
volume={9},
number={5},
pages={987--1000},
year={1998},
publisher={IEEE}
}
@article{raissi2017physics,
title={Physics informed deep learning (part i): Data-driven solutions of nonlinear partial differential equations},
author={Raissi, Maziar and Perdikaris, Paris and Karniadakis, George Em},
journal={arXiv preprint arXiv:1711.10561},
year={2017}
}
@article{BlechschmidtErnst2021,
title={Three ways to solve partial differential equations with neural networks --- A review},
author={Blechschmidt, Jan and Ernst, Oliver},
journal={GAMM‐Mitteilungen},
number={44},
year={2021},
publisher={Wiley Online Library}
}
@article{BeckETal2021,
title={Solving the Kolmogorov PDE by Means of Deep Learning},
author={Beck, Christian and Becker, Sebastian and Grohs, Philipp and Jentzen, Arnulf},
journal={Journal of Scientific Computing},
volume = {88},
number={73},
year={2021},
publisher={Springer}
}
@article{han2017deep,
title={Deep learning-based numerical methods for high-dimensional parabolic partial differential equations and backward stochastic differential equations},
author={Han, Jiequn and Jentzen, Arnulf and others},
journal={Communications in mathematics and statistics},
volume={5},
number={4},
pages={349--380},
year={2017},
publisher={Springer}
}
@article{kwon2021deep,
title={A Deep Neural Network Based on ResNet for Predicting Solutions of Poisson--Boltzmann Equation},
author={Kwon, In and Jo, Gwanghyun and Shin, Kwang-Seong},
journal={Electronics},
volume={10},
number={21},
pages={2627},
year={2021},
publisher={MDPI}
}
@article{jagtap2020conservative,
title={Conservative physics-informed neural networks on discrete domains for conservation laws: Applications to forward and inverse problems},
author={Jagtap, Ameya D and Kharazmi, Ehsan and Karniadakis, George Em},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={365},
pages={113028},
year={2020},
publisher={Elsevier}
}
@inproceedings{jagtap2021extended,
title={Extended Physics-informed Neural Networks (XPINNs): A Generalized Space-Time Domain Decomposition based Deep Learning Framework for Nonlinear Partial Differential Equations.},
author={Jagtap, Ameya D and Karniadakis, George E},
booktitle={AAAI Spring Symposium: MLPS},
year={2021}
}
@article{kharazmi2021hp,
title={hp-VPINNs: Variational physics-informed neural networks with domain decomposition},
author={Kharazmi, Ehsan and Zhang, Zhongqiang and Karniadakis, George Em},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={374},
pages={113547},
year={2021},
publisher={Elsevier}
}
@article{bardhan2011mathematical,
title={Mathematical analysis of the BIBEE approximation for molecular solvation: Exact results for spherical inclusions},
author={Bardhan, Jaydeep P and Knepley, Matthew G},
journal={arXiv preprint arXiv:1109.0651},
year={2011}
}
@article{chuang2022experience,
title={Experience report of physics-informed neural networks in fluid simulations: pitfalls and frustration},
author={Chuang, Pi-Yueh and Barba, Lorena A},
journal={arXiv preprint arXiv:2205.14249},
year={2022}
}
@article{wong2009mm,
title={MM-PBSA captures key role of intercalating water molecules at a protein- protein interface},
author={Wong, Sergio and Amaro, Rommie E and McCammon, J Andrew},
journal={Journal of chemical theory and computation},
volume={5},
number={2},
pages={422--429},
year={2009},
publisher={ACS Publications}
}
@article{andrio2019bioexcel,
title={BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows},
author={Andrio, Pau and Hospital, Adam and Conejero, Javier and Jord{\'a}, Luis and Del Pino, Marc and Codo, Laia and Soiland-Reyes, Stian and Goble, Carole and Lezzi, Daniele and Badia, Rosa M and others},
journal={Scientific data},
volume={6},
number={1},
pages={1--8},
year={2019},
publisher={Nature Publishing Group}
}
@article{marrink2007martini,
title={The MARTINI force field: coarse grained model for biomolecular simulations},
author={Marrink, Siewert J and Risselada, H Jelger and Yefimov, Serge and Tieleman, D Peter and De Vries, Alex H},
journal={The journal of physical chemistry B},
volume={111},
number={27},
pages={7812--7824},
year={2007},
publisher={ACS Publications}
}
@article{darre2015sirah,
title={SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics},
author={Darr{\'e}, Leonardo and Machado, Mat{\'\i}as Rodrigo and Brandner, Astrid Febe and Gonz{\'a}lez, Humberto Carlos and Ferreira, Sebasti{\'a}n and Pantano, Sergio},
journal={Journal of chemical theory and computation},
volume={11},
number={2},
pages={723--739},
year={2015},
publisher={ACS Publications}
}
@article{sommer2011coarse,
title={Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes},
author={Sommer, Bj{\"o}rn and Dingersen, Tim and Gamroth, Christian and Heissmann, Andr{\'e} J and Lukat, Gunther and Rotzoll, Ralf and Rubert, Sebastian and Sch{\"a}fer, Alexander and Kr{\"u}ger, Jens},
journal={Journal of Cheminformatics},
volume={3},
number={1},
pages={1--1},
year={2011},
publisher={Springer}
}
@article{li2017delphiforce,
title={DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding},
author={Li, Lin and Chakravorty, Arghya and Alexov, Emil},
journal={Journal of computational chemistry},
volume={38},
number={9},
pages={584--593},
year={2017},
publisher={Wiley Online Library}
}