Computational protein structure refinement: almost there, yet still so far to go
M Feig - Wiley Interdisciplinary Reviews: Computational …, 2017 - Wiley Online Library
Protein structures are essential in modern biology yet experimental methods are far from
being able to catch up with the rapid increase in available genomic data. Computational …
being able to catch up with the rapid increase in available genomic data. Computational …
Methods for the refinement of protein structure 3D models
R Adiyaman, LJ McGuffin - International journal of molecular sciences, 2019 - mdpi.com
The refinement of predicted 3D protein models is crucial in bringing them closer towards
experimental accuracy for further computational studies. Refinement approaches can be …
experimental accuracy for further computational studies. Refinement approaches can be …
3Drefine: an interactive web server for efficient protein structure refinement
D Bhattacharya, J Nowotny, R Cao… - Nucleic acids …, 2016 - academic.oup.com
Abstract 3Drefine is an interactive web server for consistent and computationally efficient
protein structure refinement with the capability to perform web-based statistical and visual …
protein structure refinement with the capability to perform web-based statistical and visual …
Design of a multi-epitope vaccine against SARS-CoV-2 using immunoinformatics approach
S Sanami, M Zandi, B Pourhossein, GR Mobini… - International journal of …, 2020 - Elsevier
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused COVID-19 disease
in China. So far, no vaccine has licensed to protect against infection with COVID-19 …
in China. So far, no vaccine has licensed to protect against infection with COVID-19 …
3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization
D Bhattacharya, J Cheng - Proteins: Structure, Function, and …, 2013 - Wiley Online Library
One of the major limitations of computational protein structure prediction is the deviation of
predicted models from their experimentally derived true, native structures. The limitations …
predicted models from their experimentally derived true, native structures. The limitations …
Identification of the Zn2+ binding site and mode of operation of a mammalian Zn2+ transporter
Vesicular zinc transporters (ZnTs) play a critical role in regulating Zn 2+ homeostasis in
various cellular compartments and are linked to major diseases ranging from Alzheimer …
various cellular compartments and are linked to major diseases ranging from Alzheimer …
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
The KoBaMIN web server provides an online interface to a simple, consistent and
computationally efficient protein structure refinement protocol based on minimization of a …
computationally efficient protein structure refinement protocol based on minimization of a …
Automated server predictions in CASP7
With each round of CASP (Critical Assessment of Techniques for Protein Structure
Prediction), automated prediction servers have played an increasingly important role. Today …
Prediction), automated prediction servers have played an increasingly important role. Today …
BALL-biochemical algorithms library 1.3
A Hildebrandt, AK Dehof, A Rurainski, A Bertsch… - BMC …, 2010 - Springer
Abstract Background The Biochemical Algorithms Library (BALL) is a comprehensive rapid
application development framework for structural bioinformatics. It provides an extensive …
application development framework for structural bioinformatics. It provides an extensive …
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
Motivation Protein model quality estimation, in many ways, informs protein structure
prediction. Despite their tight coupling, existing model quality estimation methods do not …
prediction. Despite their tight coupling, existing model quality estimation methods do not …