Author details

Full Name

Genki Terashi

Affiliation

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
38066344	DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.	Nat Methods	2024
37161061	DAQ-Score Database: assessment of map-model compatibility for protein structure models from cryo-EM maps.	Nat Methods	2023
37905971	Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.	Proteins	2023
37904978	Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction.	bioRxiv	2023
37783885	CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.		2023
37549063	Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.	Bioinformatics	2023
36623922	Bioinformatic Approaches for Characterizing Molecular Structure and Function of Food Proteins.	Annu Rev Food Sci Technol	2023
37365936	Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.	Proteomics	2023
36601803	Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.	Acta Crystallogr D Struct Biol	2023
34959149	Surface-based protein domains retrieval methods from a SHREC2021 challenge.	J Mol Graph Model	2022
35849043	Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.	Curr Protoc	2022
35959463	MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.	Front Mol Biosci	2022
35953671	Residue-wise local quality estimation for protein models from cryo-EM maps.	Nat Methods	2022
35383281	Real-time structure search and structure classification for AlphaFold protein models.	Commun Biol	2022
33863902	Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning.	Nat Commun	2021
35874311	CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.	Matter	2021
33542514	Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.	Nat Methods	2021
33787852	Protein contact map refinement for improving structure prediction using generative adversarial networks.	Bioinformatics	2021
33517444	Genotype & phenotype in Lowe Syndrome: specific OCRL1 patient mutations differentially impact cellular phenotypes.	Hum Mol Genet	2021
33828153	Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction.	Sci Rep	2021
33828103	VESPER: global and local cryo-EM map alignment using local density vectors.	Nat Commun	2021
34142833	Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.	J Chem Inf Model	2021
32621234	Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin.	Methods Mol Biol	2020
31746961	Protein docking model evaluation by 3D deep convolutional neural networks.	Bioinformatics	2020
31697428	Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46.	Proteins	2020
32197044	MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.	J Chem Inf Model	2020
31583633	Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes.	Methods Mol Biol	2020
31358979	Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.	Nat Methods	2019
31582626	Geometrical Conversion of the EGFR Extracellular Domain by Adiabatic Mapping Combining Normal Mode Analysis of the Elastic Network Model and Energy Optimization.	Chemical and Pharmaceutical Bulletin	2019
31612567	Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.	Proteins	2019
29691408	De novo main-chain modeling for EM maps using MAINMAST.	Nat Commun	2018
28833585	Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.	Proteins	2018
30075190	De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.	J Struct Biol	2018
29329283	Modeling the assembly order of multimeric heteroprotein complexes.	PLoS Comput Biol	2018
28262392	Variability of Protein Structure Models from Electron Microscopy.	Structure	2017
28394890	Modeling disordered protein interactions from biophysical principles.	PLoS Comput Biol	2017
27654025	Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.	Proteins	2017
27491540	Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.	BMC Structural Biology	2016
26502070	CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.	PLoS ONE	2015
25087626	Quality assessment methods for 3D protein structure models based on a residue-residue distance matrix prediction.	Chemical and Pharmaceutical Bulletin	2014
23843247	Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.	Proteins	2013
23124558	United3D: a protein model quality assessment program that uses two consensus based methods.	Chemical and Pharmaceutical Bulletin	2012
22509779	LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value.	Journal of Computational Biology	2012
22001016	Community-wide assessment of protein-interface modeling suggests improvements to design methodology.	J Mol Biol	2011
20118576	New protein structure model evaluation methods that include a side-chain consensus score for the protein modeling.	Chemical and Pharmaceutical Bulletin	2010
20045969	HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method.	Chemical and Pharmaceutical Bulletin	2010
20045957	Method for predicting homology modeling accuracy from amino acid sequence alignment: the power function.	Chemical and Pharmaceutical Bulletin	2010
19952440	FAMSD: A powerful protein modeling platform that combines alignment methods, homology modeling, 3D structure quality estimation and molecular dynamics.	Chemical and Pharmaceutical Bulletin	2009
18451572	Bioinformatics based Ligand-Docking and in-silico screening.	Chemical and Pharmaceutical Bulletin	2008
17894329	Fams-ace: a combined method to select the best model after remodeling all server models.	Proteins: Structure, Function and Bioinformatics	2007