Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology Article Swipe

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Sarel J. Fleishman , Timothy A. Whitehead , Eva‐Maria Strauch , Jacob E. Corn , Sanbo Qin , Huan‐Xiang Zhou , Julie C. Mitchell , Omar Demerdash , Mayuko Takeda‐Shitaka , Genki Terashi , Iain H. Moal , Xiaofan Li , Paul A. Bates , Martin Zacharias , Hahnbeom Park , Jun-su Ko , Hasup Lee , Chaok Seok , Thomas Bourquard , Julie Bernauer , Anne Poupon , Jérôme Azé , Seren Soner , Şefik Kerem Ovalı , Pemra Özbek , Nir Ben‐Tal , Türkan Haliloǧlu , Howook Hwang , Thom Vreven , Brian G. Pierce , Zhiping Weng , Laura Pérez‐Cano ·

YOU? · · 2020 · Open Access · · DOI: https://doi.org/10.17615/35z7-9284

The CAPRI and CASP prediction experiments have demonstrated the power of community wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting there may be important physical chemistry missing in the energy calculations. 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the non-polar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were on average structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a non-binder.

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Interface (matter) Computer science Systems engineering Engineering Bubble Parallel computing Maximum bubble pressure method

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Language: en
Landing Page: https://doi.org/10.17615/35z7-9284
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Related Works: 10
OpenAlex ID: https://openalex.org/W4301905496

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DOI: https://doi.org/10.17615/35z7-9284

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Title: Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

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Publication year: 2020

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Publication date: 2020-11-04

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Authors: Sarel J. Fleishman, Timothy A. Whitehead, Eva‐Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan‐Xiang Zhou, Julie C. Mitchell, Omar Demerdash, Mayuko Takeda‐Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Şefik Kerem Ovalı, Pemra Özbek, Nir Ben‐Tal, Türkan Haliloǧlu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Pérez‐Cano

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Landing page: https://doi.org/10.17615/35z7-9284

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Concepts: Interface (matter), Computer science, Systems engineering, Engineering, Bubble, Parallel computing, Maximum bubble pressure method

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abstract_inverted_index.very	29, 52, 81
abstract_inverted_index.were	186
abstract_inverted_index.what	117
abstract_inverted_index.wide	12, 46
abstract_inverted_index.with	80
abstract_inverted_index.CAPRI	1
abstract_inverted_index.These	213
abstract_inverted_index.areas	31
abstract_inverted_index.asked	133
abstract_inverted_index.bring	41
abstract_inverted_index.found	150, 180
abstract_inverted_index.power	9, 43
abstract_inverted_index.sets.	147
abstract_inverted_index.state	20
abstract_inverted_index.still	226
abstract_inverted_index.terms	155
abstract_inverted_index.tests	13
abstract_inverted_index.there	97, 224
abstract_inverted_index.which	87, 236
abstract_inverted_index.Beyond	174
abstract_inverted_index.and/or	139
abstract_inverted_index.appear	90
abstract_inverted_index.design	55, 221
abstract_inverted_index.energy	106
abstract_inverted_index.formed	93
abstract_inverted_index.groups	110
abstract_inverted_index.number	75
abstract_inverted_index.sought	39
abstract_inverted_index.average	188
abstract_inverted_index.between	144
abstract_inverted_index.binding	84, 184
abstract_inverted_index.current	19, 66
abstract_inverted_index.designs	159
abstract_inverted_index.docking	34
abstract_inverted_index.equally	62
abstract_inverted_index.improve	219
abstract_inverted_index.largely	164
abstract_inverted_index.metrics	245
abstract_inverted_index.missing	103
abstract_inverted_index.natural	162
abstract_inverted_index.problem	56
abstract_inverted_index.protein	33, 54
abstract_inverted_index.results	214
abstract_inverted_index.surface	204
abstract_inverted_index.backbone	198
abstract_inverted_index.complex,	235
abstract_inverted_index.computed	83
abstract_inverted_index.designed	77, 125, 172, 183, 194, 203, 211, 234
abstract_inverted_index.embedded	191
abstract_inverted_index.energies	85
abstract_inverted_index.example,	232
abstract_inverted_index.features	141
abstract_inverted_index.identify	136
abstract_inverted_index.learned;	230
abstract_inverted_index.missing:	119
abstract_inverted_index.physical	101
abstract_inverted_index.polarity	176
abstract_inverted_index.progress	26
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abstract_inverted_index.provides	58
abstract_inverted_index.research	109
abstract_inverted_index.rigidity	200
abstract_inverted_index.spurring	25
abstract_inverted_index.surfaces	185
abstract_inverted_index.assessing	17
abstract_inverted_index.challenge	114
abstract_inverted_index.character	169
abstract_inverted_index.chemistry	102
abstract_inverted_index.community	11, 45, 149, 179
abstract_inverted_index.complexes	126, 131
abstract_inverted_index.energetic	137
abstract_inverted_index.favorable	82
abstract_inverted_index.function.	212
abstract_inverted_index.generated	73
abstract_inverted_index.important	100, 206
abstract_inverted_index.monomers,	195
abstract_inverted_index.naturally	129
abstract_inverted_index.non-polar	168
abstract_inverted_index.occurring	130
abstract_inverted_index.partially	156
abstract_inverted_index.solvation	154
abstract_inverted_index.structure	36
abstract_inverted_index.classified	242
abstract_inverted_index.complexes,	163
abstract_inverted_index.interfaces	79
abstract_inverted_index.prediction	4
abstract_inverted_index.structural	140
abstract_inverted_index.structures	122
abstract_inverted_index.suggesting	96, 196
abstract_inverted_index.challenging	30, 53
abstract_inverted_index.determining	116
abstract_inverted_index.difference,	177
abstract_inverted_index.distinguish	143, 157
abstract_inverted_index.experiments	5, 47
abstract_inverted_index.fundamental	63
abstract_inverted_index.methodology	15
abstract_inverted_index.non-binder.	248
abstract_inverted_index.prediction.	37
abstract_inverted_index.realization	208
abstract_inverted_index.strategies,	222
abstract_inverted_index.demonstrated	7
abstract_inverted_index.experiments,	95, 240
abstract_inverted_index.participants	134
abstract_inverted_index.structurally	189
abstract_inverted_index.calculations.	107
abstract_inverted_index.complementary	60
abstract_inverted_index.computational	220
abstract_inverted_index.contributions	138
abstract_inverted_index.interactions.	173
abstract_inverted_index.understanding	67
abstract_inverted_index.conformational	199
abstract_inverted_index.electrostatics	152
abstract_inverted_index.protein-binding	69
abstract_inverted_index.protein-protein	78
abstract_inverted_index.thermodynamics.	70
cited_by_percentile_year
countries_distinct_count	0
institutions_distinct_count	32
citation_normalized_percentile.value	0.22188915
citation_normalized_percentile.is_in_top_1_percent	False
citation_normalized_percentile.is_in_top_10_percent	False