19 research outputs found
ChatGPT Chemistry Assistant for Text Mining and Prediction of MOF Synthesis
We use prompt engineering to guide ChatGPT in the automation of text mining
of metal-organic frameworks (MOFs) synthesis conditions from diverse formats
and styles of the scientific literature. This effectively mitigates ChatGPT's
tendency to hallucinate information -- an issue that previously made the use of
Large Language Models (LLMs) in scientific fields challenging. Our approach
involves the development of a workflow implementing three different processes
for text mining, programmed by ChatGPT itself. All of them enable parsing,
searching, filtering, classification, summarization, and data unification with
different tradeoffs between labor, speed, and accuracy. We deploy this system
to extract 26,257 distinct synthesis parameters pertaining to approximately 800
MOFs sourced from peer-reviewed research articles. This process incorporates
our ChemPrompt Engineering strategy to instruct ChatGPT in text mining,
resulting in impressive precision, recall, and F1 scores of 90-99%.
Furthermore, with the dataset built by text mining, we constructed a
machine-learning model with over 86% accuracy in predicting MOF experimental
crystallization outcomes and preliminarily identifying important factors in MOF
crystallization. We also developed a reliable data-grounded MOF chatbot to
answer questions on chemical reactions and synthesis procedures. Given that the
process of using ChatGPT reliably mines and tabulates diverse MOF synthesis
information in a unified format, while using only narrative language requiring
no coding expertise, we anticipate that our ChatGPT Chemistry Assistant will be
very useful across various other chemistry sub-disciplines.Comment: Published on Journal of the American Chemical Society (2023); 102
pages (18-page manuscript, 84 pages of supporting information
Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data
We have developed a Generative Recurrent Neural Networks (GRNN) that learns
the probability of the next residue torsions $X_{i+1}=\
[\phi_{i+1},\psi_{i+1},\omega _{i+1}, \chi_{i+1}]X_i$ to generate new IDP conformations. In addition, we couple
the GRNN with a Bayesian model, X-EISD, in a reinforcement learning step that
biases the probability distributions of torsions to take advantage of
experimental data types such as J-couplingss, NOEs and PREs. We show that
updating the generative model parameters according to the reward feedback on
the basis of the agreement between structures and data improves upon existing
approaches that simply reweight static structural pools for disordered
proteins. Instead the GRNN "DynamICE" model learns to physically change the
conformations of the underlying pool to those that better agree with
experiment
Learning Correlations between Internal Coordinates to Improve 3D Cartesian Coordinates for Proteins.
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Learning Correlations between Internal Coordinates to Improve 3D Cartesian Coordinates for Proteins.
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the internal-to-Cartesian process relies on correctly predicting chemically subtle correlations among the internal coordinates themselves, and learning these correlations increases the fidelity of the Cartesian representation. We developed a machine learning algorithm, Int2Cart, to predict bond lengths and bond angles from backbone torsion angles and residue types of a protein, which allows reconstruction of protein structures better than using fixed bond lengths and bond angles or a static library method that relies on backbone torsion angles and residue types in a local environment. The method is able to be used for structure validation, as we show that the agreement between Int2Cart-predicted bond geometries and those from an AlphaFold 2 model can be used to estimate model quality. Additionally, by using Int2Cart to reconstruct an IDP ensemble, we are able to decrease the clash rate during modeling. The Int2Cart algorithm has been implemented as a publicly accessible python package at https://github.com/THGLab/int2cart
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Protein Dynamics to Define and Refine Disordered Protein Ensembles
Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse R2 relaxation rates and Lipari-Szabo order parameters (S2 values). We illustrate our approach using the unfolded state of the drkN SH3 domain to show that the dynamical ensembles give better agreement than a static ensemble for a wide range of experimental validation data including NMR chemical shifts, J-couplings, nuclear Overhauser effects, paramagnetic relaxation enhancements, residual dipolar couplings, hydrodynamic radii, single-molecule fluorescence Förster resonance energy transfer, and small-angle X-ray scattering
A benchmark dataset for Hydrogen Combustion.
The generation of reference data for deep learning models is challenging for reactive systems, and more so for combustion reactions due to the extreme conditions that create radical species and alternative spin states during the combustion process. Here, we extend intrinsic reaction coordinate (IRC) calculations with ab initio MD simulations and normal mode displacement calculations to more extensively cover the potential energy surface for 19 reaction channels for hydrogen combustion. A total of ∼290,000 potential energies and ∼1,270,000 nuclear force vectors are evaluated with a high quality range-separated hybrid density functional, ωB97X-V, to construct the reference data set, including transition state ensembles, for the deep learning models to study hydrogen combustion reaction
IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.
The power of structural information for informing biological mechanisms is clear for stable folded macromolecules, but similar structure-function insight is more difficult to obtain for highly dynamic systems such as intrinsically disordered proteins (IDPs) which must be described as structural ensembles. Here, we present IDPConformerGenerator, a flexible, modular open-source software platform for generating large and diverse ensembles of disordered protein states that builds conformers that obey geometric, steric, and other physical restraints on the input sequence. IDPConformerGenerator samples backbone phi (φ), psi (ψ), and omega (ω) torsion angles of relevant sequence fragments from loops and secondary structure elements extracted from folded protein structures in the RCSB Protein Data Bank and builds side chains from robust Monte Carlo algorithms using expanded rotamer libraries. IDPConformerGenerator has many user-defined options enabling variable fractional sampling of secondary structures, supports Bayesian models for assessing the agreement of IDP ensembles for consistency with experimental data, and introduces a machine learning approach to transform between internal and Cartesian coordinates with reduced error. IDPConformerGenerator will facilitate the characterization of disordered proteins to ultimately provide structural insights into these states that have key biological functions