Results 61 to 70 of about 410,461 (311)

Prediction of Protein Function Using Statistically Significant Sub-Structure Discovery [PDF]

, 2007
Proteins perform a vast number of functional roles. The number of protein structures available for analysis continues to grow and, with the development of methods to predict protein structure directly from genetic sequence without imaging technology, the
Lucas, Craig
core  

Structure prediction of alternative protein conformations

Nature Communications
Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB.
Patrick Bryant, Frank Noé
doaj   +1 more source

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Frontiers in Molecular Biosciences, 2021
Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design.
Farhan Quadir, Raj S. Roy, Elham Soltanikazemi, Jianlin Cheng   +3 more
doaj   +1 more source

The planar cell polarity protein Vangl2 interacts with the PDZ‐domains of Scribble but not with a unique PDZ‐like domain in Inturned

FEBS Letters, EarlyView.
Structural and biochemical characterisations show that the planar cell polarity (PCP) protein Inturned harbours a unique PDZ‐like domain that does not bind canonical PDZ‐binding motifs (PBMs) like that of another PCP protein Vangl2. In contrast, the apical‐basal polarity protein Scribble contains four PDZ domains that bind Vangl2, but one PDZ domain ...
Stephan Wilmes, Jan Brysch, Carmen Gelze, Lilli Meier, Daniel Kümmel   +4 more
wiley   +1 more source

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction

Frontiers in Molecular Biosciences, 2021
Protein-protein docking is a useful tool for modeling the structures of protein complexes that have yet to be experimentally determined. Understanding the structures of protein complexes is a key component for formulating hypotheses in biophysics ...
Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara, Daisuke Kihara   +4 more
doaj   +1 more source

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction

, 2008
Background: We present a novel method of protein fold decoy discrimination using machine learning, more specifically using neural networks. Here, decoy discrimination is represented as a machine learning problem, where neural networks are used to learn ...
Jones, DT, Tan Ching-Wai, Jones David T, Tan, CW   +3 more
core   +1 more source

Local protein structure prediction using discriminative models

BMC Bioinformatics, 2006
Background In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition incorporation of local structure ...
Lengauer Thomas, Sommer Ingolf, Sander Oliver   +2 more
doaj   +1 more source

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

FEBS Letters, EarlyView.
A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa, Konstantinos Makryniotis, Theofani‐Iosifina Sousani, Evangelos Topakas, Vangelis Daskalakis, Maria Dimarogona   +5 more
wiley   +1 more source

CHCHD4 Oxidoreductase Activity: A Comprehensive Analysis of the Molecular, Functional, and Structural Properties of Its Redox-Regulated Substrates

Molecules
The human CHCHD4 protein, which is a prototypical family member, carries a coiled–coil–helix–coiled–coil–helix motif that is stabilized by two disulfide bonds.
Nicole Balasco, Nazanine Modjtahedi, Alessandra Monti, Menotti Ruvo, Luigi Vitagliano, Nunzianna Doti   +5 more
doaj   +1 more source