100 Result(s)

Article

Geometry-complete diffusion for 3D molecule generation and optimization

Generative deep learning methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a denoising diffusion framework. However, such methods are unable ...

Alex Morehead, Jianlin Cheng in Communications Chemistry (2024)

Article

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking acc...

Nabin Giri, Jianlin Cheng in Nature Communications (2024)

Article

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomi...

Nabin Giri, Liguo Wang, Jianlin Cheng in Scientific Data (2024)

Article

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and re...

Jian Liu, Zhiye Guo, Tianqi Wu, Raj S. Roy, Farhan Quadir… in Communications Biology (2023)

Article

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to fu...

Jian Liu, Zhiye Guo, Tianqi Wu, Raj S. Roy, Chen Chen… in Communications Chemistry (2023)

Article

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222₁ and P

Cole E. McKay, Jianlin Cheng, John J. Tanner in Scientific Reports (2023)

Article

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

In this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset o...

Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng in Scientific Data (2023)

Article

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in ...

Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng in Scientific Data (2023)

Article

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict in...

Zhiye Guo, Jian Liu, Jeffrey Skolnick, Jianlin Cheng in Nature Communications (2022)

Article

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

The information about the domain architecture of proteins is useful for studying protein structure and function. However, accurate prediction of protein domain boundaries (i.e., sequence regions separating two...

Sajid Mahmud, Zhiye Guo, Farhan Quadir, Jian Liu, Jianlin Cheng in BMC Bioinformatics (2022)

Article

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

The genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Pre...

**aowen Shi, Hua Yang, Chen Chen, Jie Hou, Tieming Ji… in Nature Communications (2022)

Article

Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii

Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under hig...

Ningning Zhang, Erin M. Mattoon, Will McHargue, Benedikt Venn… in Communications Biology (2022)

Article

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure feat...

**ao Chen, Jianlin Cheng in BMC Bioinformatics (2022)

Article

Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction

Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng in BMC Bioinformatics (2022)

Article

De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays)

The B chromosome of maize undergoes nondisjunction at the second pollen mitosis as part of its accumulation mechanism. Previous work identified 9-Bic-1 (9-B inactivated centromere-1), which comprises an epigen...

Ryan N. Douglas, Hua Yang, Bing Zhang, Chen Chen, Fangpu Han… in Chromosome Research (2021)

Article

Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network

Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng in BMC Bioinformatics (2021)

Article

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly av...

Tianqi Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng in Scientific Reports (2021)

Article

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple seque...

Farhan Quadir, Raj S. Roy, Randal Halfmann, Jianlin Cheng in Scientific Reports (2021)

Article

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To ...

**ao Chen, Jian Liu, Zhiye Guo, Tianqi Wu, Jie Hou, Jianlin Cheng in Scientific Reports (2021)