Evidence map›Paper›PMID 40044686›Full record

ArticleNature communications2025

A robust crystal structure prediction method to support small molecule drug development with large scale validation and blind study.

Dong Zhou, Imanuel Bier, Biswajit Santra, Leif D Jacobson, Chuanjie Wu, Adiran Garaizar Suarez, Barbara Ramirez Almaguer, Haoyu Yu, Robert Abel, Richard A Friesner and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Dong ZhouSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Imanuel BierSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Biswajit SantraSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Leif D JacobsonSchrödinger Inc., Portland: 101 SW Main Street, Suite 1300, 97204, Portland, OR, USA.
Chuanjie WuSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Adiran Garaizar SuarezBayer AG, Computational Life Science, Alfred-Nobel-Straße 50, 40789, 40789, Monheim am Rhein, Germany.
Barbara Ramirez AlmaguerBayer AG, Process Industrialization, Friedrich-Ebert-Str. 217, 42117, Wuppertal, Germany.
Haoyu YuSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Robert AbelSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.
Richard A FriesnerDepartment of Chemistry, Columbia University, New York, 10027, New York, USA.
Lingle WangSchrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA. Lingle.wang@schrodinger.com.ORCID http://orcid.org/0000-0002-8170-6798

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Crystal polymorphism is an important and fascinating aspect of solid state chemistry with far reaching implications in the pharmaceuticals, agrisciences, nutraceuticals, battery and aviation industries. Late appearing more stable polymorphs have caused numerous issues in the pharmaceutical industry. Experimental polymorph screening can be very expensive and time consuming, and sometimes may miss important low energy polymorphs due to an inability to exhaust all crystallization conditions. In this paper, we report a crystal structure prediction (CSP) method with state of the art accuracy and efficiency, validated on a large and diverse dataset including 66 molecules with 137 experimentally known polymorphic forms. The method combines a novel systematic crystal packing search algorithm and the use of machine learning force fields in a hierarchical crystal energy ranking. Our method not only reproduces all the experimentally known polymorphs, but also suggests new low energy polymorphs yet to be discovered by experiment that might pose potential risks to development of the currently known forms of these compounds. In addition, we report the prediction results of a blinded study, results for Target XXXI from the seventh CSP blind test, and demonstrate how the method can be used to accelerate clinical formulation design and derisk downstream processing.

Indexed as

Drug DevelopmentSmall Molecule LibrariesAlgorithmsCrystallizationCrystallography, X-RayMachine LearningModels, MolecularPharmaceutical PreparationsPharmaceutical PreparationsSmall Molecule Libraries

Identifiers

PMID40044686
PMCPMC11882951

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LicenceCC BY-NC-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.