[HTML][HTML] Antibody structure and function: the basis for engineering therapeutics

ML Chiu, DR Goulet, A Teplyakov, GL Gilliland - Antibodies, 2019‏ - mdpi.com
Antibodies and antibody-derived macromolecules have established themselves as the
mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure …

Electrostatic interactions in protein structure, folding, binding, and condensation

HX Zhou, X Pang - Chemical reviews, 2018‏ - ACS Publications
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

I Johansson-Åkhe, B Wallner - Frontiers in bioinformatics, 2022‏ - frontiersin.org
Protein interactions are key in vital biological processes. In many cases, particularly in
regulation, this interaction is between a protein and a shorter peptide fragment. Such …

The structural basis of antibody-antigen recognition

I Sela-Culang, V Kunik, Y Ofran - Frontiers in immunology, 2013‏ - frontiersin.org
The function of antibodies (Abs) involves specific binding to antigens (Ags) and activation of
other components of the immune system to fight pathogens. The six hypervariable loops …

Hirshfeld surface analysis

MA Spackman, D Jayatilaka - CrystEngComm, 2009‏ - pubs.rsc.org
In the last few years the analysis of molecular crystal structures using tools based on
Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to …

Anatomy of hot spots in protein interfaces

AA Bogan, KS Thorn - Journal of molecular biology, 1998‏ - Elsevier
Binding of one protein to another is involved in nearly all biological functions, yet the
principles governing the interaction of proteins are not fully understood. To analyze the …

How TCRs bind MHCs, peptides, and coreceptors

MG Rudolph, RL Stanfield, IA Wilson - Annu. Rev. Immunol., 2006‏ - annualreviews.org
Since the first crystal structure determinations of αβ T cell receptors (TCRs) bound to class I
MHC-peptide (pMHC) antigens in 1996, a sizable database of 24 class I and class II …

Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals

MA Spackman, JJ McKinnon, D Jayatilaka - CrystEngComm, 2008‏ - pubs.rsc.org
Ab initio electrostatic potentials for molecules can readily be mapped onto their Hirshfeld
surfaces and displayed within a crystal packing diagram. In this manner the close molecular …

The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology

F Fogolari, A Brigo, H Molinari - Journal of Molecular …, 2002‏ - Wiley Online Library
Electrostatics plays a fundamental role in virtually all processes involving biomolecules in
solution. The Poisson–Boltzmann equation constitutes one of the most fundamental …

Close‐range electrostatic interactions in proteins

S Kumar, R Nussinov - ChemBioChem, 2002‏ - Wiley Online Library
Two types of noncovalent bonding interactions are present in protein structures, specific and
nonspecific. Nonspecific interactions are mostly hydrophobic and van der Waals. Specific …