In recent years, it has been demonstrated that proteins with new functionality or shapes can be designed via structure-based modeling methods, and the design strategies have combined all available information —
protein stabilityA structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native...
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust p
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust p
acyltransferases and formed a relatively distinct branch, indicating its high sequence specificity (Fig.1a, b). The distribution of AmAT7-3, AmAT8-17, and the six known glycoside ATs explained the challenges in predicting the function of an acetyltransferase solely based on its protein sequence. ...
co-evolution protein design homology modeling Introduction Proteins are linear polymers that fold into very specific and ordered three-dimensional (3D) conformations based on their amino acid sequence (Branden and Tooze, 1999, Dill, 1990). Understanding how this occurs is a foundational problem in bi...
Identifies a protein's fold by comparing its sequence with known structures. Applications Functional Annotation Drug Design Protein Engineering Drug Target Identification Membrane Protein Function Study Biophysics Research Antibody Drug Development Immunotherapy Diagnostic Assays Therapeutic Applications Biotechnology ...
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored...
The protein universe in 3D Predicting protein structures from amino acid sequences used to be difficult and error prone. This changed in 2021 when AlphaFold2 reported near-experimental accuracy for most single-domain proteins. We look back on this breakthrough, discuss its effect on the field, ...
protein sequence (or the corresponding 3D structure), overcoming the limitations of standard feature-based machine learning (ML) methods. The majority of sequence-based protein function prediction methods use 1D CNNs, or variations thereof, that search for recurring spatial patterns within a given ...