Before and after AlphaFold2: An overview of protein structure prediction

LMF Bertoline, AN Lima, JE Krieger… - Frontiers in …, 2023 - frontiersin.org
Three-dimensional protein structure is directly correlated with its function and its
determination is critical to understanding biological processes and addressing human …

[HTML][HTML] CADD, AI and ML in drug discovery: A comprehensive review

D Vemula, P Jayasurya, V Sushmitha, YN Kumar… - European Journal of …, 2023 - Elsevier
Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest
because of its potential to expedite and lower the cost of the drug development process …

[HTML][HTML] Computational methods in drug discovery

SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …

Comparative protein structure modeling using MODELLER

B Webb, A Sali - Current protocols in bioinformatics, 2016 - Wiley Online Library
Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

The PSIPRED protein structure prediction server

LJ McGuffin, K Bryson, DT Jones - Bioinformatics, 2000 - academic.oup.com
The PSIPRED protein structure prediction server allows users to submit a protein sequence,
perform a prediction of their choice and receive the results of the prediction both textually via …

Comparative protein structure modeling of genes and genomes

MA Martí-Renom, AC Stuart, A Fiser… - Annual review of …, 2000 - annualreviews.org
▪ Abstract Comparative modeling predicts the three-dimensional structure of a given protein
sequence (target) based primarily on its alignment to one or more proteins of known …

Statistical potential for assessment and prediction of protein structures

M Shen, A Sali - Protein science, 2006 - Wiley Online Library
Protein structures in the Protein Data Bank provide a wealth of data about the interactions
that determine the native states of proteins. Using the probability theory, we derive an atomic …

Modeling of loops in protein structures

A Fiser, RKG Do, A Šali - Protein science, 2000 - Wiley Online Library
Comparative protein structure prediction is limited mostly by the errors in alignment and loop
modeling. We describe here a new automated modeling technique that significantly …

QMEAN: A comprehensive scoring function for model quality assessment

P Benkert, SCE Tosatto… - … : Structure, Function, and …, 2008 - Wiley Online Library
In protein structure prediction, a considerable number of alternative models are usually
produced from which subsequently the final model has to be selected. Thus, a scoring …

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

J Gough, K Karplus, R Hughey, C Chothia - Journal of molecular biology, 2001 - Elsevier
Of the sequence comparison methods, profile-based methods perform with greater
selectively than those that use pairwise comparisons. Of the profile methods, hidden Markov …