Protein Structure Modeling with MODELLER.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0892-0_14
Abstract: Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods.… read more here.
Keywords: protein; modeling modeller; protein structure; structure modeling ... See more keywords
High-Throughput Antibody Structure Modeling and Design Using ABodyBuilder.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8736-8_21
Abstract: Antibodies are proteins of the adaptive immune system; they can be designed to bind almost any molecule, and are increasingly being used as biotherapeutics. Experimental antibody design is an expensive and time-consuming process, and computational… read more here.
Keywords: design; antibody; structure modeling; antibody structure ... See more keywords
Effective integration and models of information: lessons from integrative structure modeling
Sign Up to like & getrecommendations! Published in 2025 at "Synthese"
DOI: 10.1007/s11229-025-04911-0
Abstract: Integrative structure modeling is a method for using information from multiple sources to compute structural models of biomolecular systems. It proceeds via four steps: (i) defining the model representation, which determines the variables whose values… read more here.
Keywords: information; integration; structure modeling; lessons integrative ... See more keywords
Influence of Electronic Structure Modeling and Junction Structure on First-Principles Chiral Induced Spin Selectivity.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.0c00621
Abstract: We have carried out a comprehensive study of the influence of electronic structure modeling and junction structure description on the first-principles calculation of the spin polarization in molecular junctions caused by the chiral induced spin… read more here.
Keywords: electronic structure; structure modeling; spin; structure ... See more keywords
Conformational Dynamics of the Activated GLP-1 Receptor-Gs Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling
Sign Up to like & getrecommendations! Published in 2023 at "ACS Central Science"
DOI: 10.1021/acscentsci.3c00063
Abstract: Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging… read more here.
Keywords: linking mass; structure modeling; structure; mass spectrometry ... See more keywords
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
Sign Up to like & getrecommendations! Published in 2024 at "Nature Communications"
DOI: 10.1038/s41467-024-49647-6
Abstract: 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 accurate homologous or predicted structures as templates… read more here.
Keywords: protein structure; density maps; structure modeling; density ... See more keywords
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac372
Abstract: Abstract Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods in recent years; however, many tools developed in the field stay exclusive to only a few bioinformatic groups.… read more here.
Keywords: rna structure; structure modeling; tools online; rna ... See more keywords
Structure Modeling and Virtual Screening with HCAR3 to Discover Potential Therapeutic Molecules
Sign Up to like & getrecommendations! Published in 2025 at "Pharmaceuticals"
DOI: 10.3390/ph18091290
Abstract: Background: Hydroxycarboxylic acid receptor 3 (HCAR3) is a receptor that is mainly expressed in human adipose tissue. It can inhibit lipolysis through the inhibition of adenylyl cyclase; thus, it is closely related to the regulation… read more here.
Keywords: receptor; umbrella sampling; virtual screening; structure modeling ... See more keywords