Binding affinity prediction of nanobody–protein complexes by scoring of molecular dynamics trajectories
Literature Information
Miguel A. Soler, Ario de Marco, Alessandro Laio
Nanobodies offer a viable alternative to antibodies for engineering high affinity binders. Their small size has an additional advantage: it allows exploiting computational protocols for optimizing their biophysical features, such as the binding affinity. The efficient prediction of this quantity is still considered a daunting task especially for modelled complexes. We show how molecular dynamics can successfully assist in the binding affinity prediction of modelled nanobody–protein complexes. The approximate initial configurations obtained by in silico design must undergo large rearrangements before achieving a stable conformation, in which the binding affinity can be meaningfully estimated. The scoring functions developed for the affinity evaluation of crystal structures will provide accurate estimates for modelled binding complexes if the scores are averaged over long finite temperature molecular dynamics simulations.
Recommended Journals

Current Opinion in Colloid & Interface Science

Acta Materialia

Organic Process Research & Development

Chemical Communications

Journal of Natural Medicines

Journal of Peptide Science

Russian Journal of Coordination Chemistry

Russian Journal of Bioorganic Chemistry

Nature Medicine

Chemistry Education Research and Practice
Related Literature
Functionalized polyesters from organocatalyzed ROP of gluOCA, the O-carboxyanhydride derived from glutamic acid
Olivier Thillaye du Boullay, Colin Bonduelle, Blanca Martin-Vaca, Didier Bourissou
DOI: 10.1039/B800852C
Macromolecular complexation of poly(methylenephosphine) to gold(i): a facile route to highly metallated polymers
Bronwyn H. Gillon, Brian O. Patrick, Derek P. Gates
DOI: 10.1039/B719199E
Single microbead SELEX for efficient ssDNA aptamer generation against botulinum neurotoxin‡
Jeffrey B.-H. Tok, Nicholas O. Fischer
DOI: 10.1039/B717936G
Lewis acid-catalyzed hydrogenation: B(C6F5)3-mediated reduction of imines and nitriles with H2‡
Preston A. Chase, Titel Jurca, Douglas W. Stephan
DOI: 10.1039/B718598G
Chromonic liquid crystals: properties and applications as functional materials
Suk-Wah Tam-Chang, Liming Huang
DOI: 10.1039/B714319B
Chemical modifications of AFM tips for the study of molecular recognition events
Régis Barattin, Normand Voyer
DOI: 10.1039/B614328H
One-step solid-state thermolysis of a metal–organic framework: a simple and facile route to large-scale of multiwalled carbon nanotubes
Linyun Chen, Junfeng Bai, Chunzhao Wang, Yi Pan, Manfred Scheer, Xiaozeng You
DOI: 10.1039/B718476J
Synthesis of metallic magnesium nanoparticles by sonoelectrochemistry
Iris Haas, Aharon Gedanken
DOI: 10.1039/B717670H
You might also like
What precautions should be taken when handling 4-Methyl-6-(trifluoromethyl)quinoline (CAS: 40716-16-3)?
When handling 4-Methyl-6-(trifluoromethyl)quinoline (CAS: 40716-16-3), safety go...
What is 4-(3,5-Difluorophenyl)aniline (CAS: 405058-00-6)?
4-(3,5-Difluorophenyl)aniline is an aromatic organic compound with the CAS numbe...
How is 5-{[4-(Trifluoromethyl)phenyl]sulfanyl}-1,2,3-thiadiazole-4-carboxylic acid (CAS: 338982-07-3) typically synthesized?
5-{[4-(Trifluoromethyl)phenyl]sulfanyl}-1,2,3-thiadiazole-4-carboxylic acid can ...
What is the market or research trend for 4-Benzylaniline hydrochloride (CAS: 6317-57-3)?
The market for 4-Benzylaniline hydrochloride (CAS: 6317-57-3) is steadily growin...
Is [3-(Diethylsulfamoyl)phenyl]boronic acid (CAS: 871329-58-7) safe?
[3-(Diethylsulfamoyl)phenyl]boronic acid is generally considered safe when handl...
What are the main uses of 3-Bromo-2,5-dimethoxyaniline (CAS: 115929-62-9)?
3-Bromo-2,5-dimethoxyaniline is mainly used in the pharmaceutical and chemical i...
What regulatory guidelines apply to N-Methyl-1-(5-methyl-1H-indol-3-yl)methanamine (CAS: 915922-67-7)?
N-Methyl-1-(5-methyl-1H-indol-3-yl)methanamine (CAS: 915922-67-7) is subject to ...
What industries use Carbamic acid, N-[(5S)-5,6-diamino-6-oxohexyl]-, 1,1-dimethylethyl ester (CAS: 24828-96-4)?
This compound is primarily used in the pharmaceutical industry for the synthesis...
How should 2-Methyl-2-propanyl [(1S,3R)-3-aminocyclohexyl]carbamate (CAS: 1298101-47-9) be stored?
2-Methyl-2-propanyl [(1S,3R)-3-aminocyclohexyl]carbamate (CAS: 1298101-47-9) sho...
What industries use Ethyl 2-bromo-4,4,4-trifluorobutanoate (CAS: 367-33-9)?
Ethyl 2-bromo-4,4,4-trifluorobutanoate (CAS: 367-33-9) is utilized in the pharma...
Source Journal
Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.



![6-Bromo-3-ethyl-3H-imidazo[4,5-b]pyridine structure 6-Bromo-3-ethyl-3H-imidazo[4,5-b]pyridine structure](https://static.chemtradehub.com/structs/103/1033202-59-3-2a8f.webp)
