Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Computer-aided design of functional protein interactions

DJ Mandell, T Kortemme - Nature chemical biology, 2009 - nature.com
Predictive methods for the computational design of proteins search for amino acid
sequences adopting desired structures that perform specific functions. Typically, design …

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

X Liu, Y Luo, P Li, S Song, J Peng - PLoS computational biology, 2021 - journals.plos.org
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew… - PloS one, 2013 - journals.plos.org
The Rosetta molecular modeling software package provides experimentally tested and
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins …

Flex ddG: Rosetta ensemble-based estimation of changes in protein–protein binding affinity upon mutation

KA Barlow, S Ó Conchúir, S Thompson… - The Journal of …, 2018 - ACS Publications
Computationally modeling changes in binding free energies upon mutation (interface ΔΔ G)
allows large-scale prediction and perturbation of protein–protein interactions. Additionally …

Regio‐and stereoselective steroid hydroxylation at C7 by cytochrome P450 monooxygenase mutants

A Li, CG Acevedo‐Rocha, L D'Amore… - Angewandte …, 2020 - Wiley Online Library
Steroidal C7β alcohols and their respective esters have shown significant promise as
neuroprotective and anti‐inflammatory agents to treat chronic neuronal damage like stroke …

AB‐bind: antibody binding mutational database for computational affinity predictions

S Sirin, JR Apgar, EM Bennett, AE Keating - Protein Science, 2016 - Wiley Online Library
Antibodies (Abs) are a crucial component of the immune system and are often used as
diagnostic and therapeutic agents. The need for high‐affinity and high‐specificity antibodies …

Computational design of a modular protein sense-response system

AA Glasgow, YM Huang, DJ Mandell, M Thompson… - Science, 2019 - science.org
Sensing and responding to signals is a fundamental ability of living systems, but despite
substantial progress in the computational design of new protein structures, there is no …

Predicting the effect of mutations on protein-protein binding interactions through structure-based interface profiles

JR Brender, Y Zhang - PLoS computational biology, 2015 - journals.plos.org
The formation of protein-protein complexes is essential for proteins to perform their
physiological functions in the cell. Mutations that prevent the proper formation of the correct …

Theoretical and computational protein design

I Samish, CM MacDermaid… - Annual review of …, 2011 - annualreviews.org
From exponentially large numbers of possible sequences, protein design seeks to identify
the properties of those that fold to predetermined structures and have targeted structural and …