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Author Details

Daisuke Kihara
Purdue University
1997
197
40
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36250895Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases.Plant Physiol2023
36250895Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases.Plant Physiol2023
37662252Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations.bioRxiv2023
37549063Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.Bioinformatics2023
36580595Opinion: Protein folds vs. protein folding: Differing questions, different challenges.Proc Natl Acad Sci U S A2023
36814641Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Front Mol Biosci2023
37450159Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server.Methods Mol Biol2023
36623922Bioinformatic Approaches for Characterizing Molecular Structure and Function of Food Proteins.Annu Rev Food Sci Technol2023
37365936Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics2023
36924867PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features.Methods2023
36601803Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.Acta Crystallogr D Struct Biol2023
36851914Computational prediction of disordered binding regions.Comput Struct Biotechnol J2023
36529945Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics2023
37161061DAQ-Score Database: assessment of map-model compatibility for protein structure models from cryo-EM maps.Nat Methods2023
37662252Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations.bioRxiv2023
37549063Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.Bioinformatics2023
37161061DAQ-Score Database: assessment of map-model compatibility for protein structure models from cryo-EM maps.Nat Methods2023
37450159Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server.Methods Mol Biol2023
37365936Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics2023
36924867PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features.Methods2023
36623922Bioinformatic Approaches for Characterizing Molecular Structure and Function of Food Proteins.Annu Rev Food Sci Technol2023
36814641Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Front Mol Biosci2023
36851914Computational prediction of disordered binding regions.Comput Struct Biotechnol J2023
36580595Opinion: Protein folds vs. protein folding: Differing questions, different challenges.Proc Natl Acad Sci U S A2023
36601803Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.Acta Crystallogr D Struct Biol2023
36529945Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics2023
34309909Benchmarking of structure refinement methods for protein complex models.Proteins2022
35849043Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Curr Protoc2022
35959463MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Front Mol Biosci2022
35953671Residue-wise local quality estimation for protein models from cryo-EM maps.Nat Methods2022
35383281Real-time structure search and structure classification for AlphaFold protein models.Commun Biol2022
36090027RL-MLZerD: Multimeric protein docking using reinforcement learning.Front Mol Biosci2022
36089054Domain-Based Protein Docking with Extremely Large Conformational Changes.J Mol Biol2022
36344967A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.BMC Biol2022
35875419ContactPFP: Protein function prediction using predicted contact information.Front Bioinform2022
35609776Multi-level analysis of intrinsically disordered protein docking methods.Methods2022
35475517Using steered molecular dynamic tension for assessing quality of computational protein structure models.J Comput Chem2022
35474753OC_Finder: Osteoclast segmentation, counting, and classification using watershed and deep learning.Front Bioinform2022
34309909Benchmarking of structure refinement methods for protein complex models.Proteins2022
34959149Surface-based protein domains retrieval methods from a SHREC2021 challenge.J Mol Graph Model2022
35383281Real-time structure search and structure classification for AlphaFold protein models.Commun Biol2022
35475517Using steered molecular dynamic tension for assessing quality of computational protein structure models.J Comput Chem2022
35474753OC_Finder: Osteoclast segmentation, counting, and classification using watershed and deep learning.Front Bioinform2022
35609776Multi-level analysis of intrinsically disordered protein docking methods.Methods2022
35849043Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Curr Protoc2022
35875419ContactPFP: Protein function prediction using predicted contact information.Front Bioinform2022
35959463MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Front Mol Biosci2022
35953671Residue-wise local quality estimation for protein models from cryo-EM maps.Nat Methods2022
36090027RL-MLZerD: Multimeric protein docking using reinforcement learning.Front Mol Biosci2022
36089054Domain-Based Protein Docking with Extremely Large Conformational Changes.J Mol Biol2022
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Collaborators

Genki Terashi
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Charles Christoffer
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Woong-Hee Shin
Co-authored papers 23
Juan Esquivel-Rodr??guez
Costa Rica Institute of Technology
Co-authored papers 18
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Aashish Jain
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College of Dentistry, Dankook University.
Co-authored papers 9
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Purdue University
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University of Missouri
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Dalton Cardiovascular Research Center, University of Missouri
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Amitava Roy
University of Montana
Co-authored papers 4
Paul A Bates
The Francis Crick Institute
Co-authored papers 4
Chaok Seok
Seoul National University
Co-authored papers 4
Sheng-You Huang
Huazhong University of Science and Technology
Co-authored papers 4
Brian G Pierce
University of Maryland Institute for Bioscience and Biotechnology Research
Co-authored papers 4
Thom Vreven
Visterra Inc.
Co-authored papers 4
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 4
Brian Jim??nez-Garc??a
Utrecht University
Co-authored papers 4
Iain H Moal
GSK Medicines Research Centre
Co-authored papers 4
Mitsuo Iwadate
Co-authored papers 3
Panagiotis L Kastritis
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Release 1.2