Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

Recent structural insights into cytochrome P450 function

FP Guengerich, MR Waterman, M Egli - Trends in pharmacological …, 2016 - cell.com
Cytochrome P450 (P450) enzymes are important in the metabolism of drugs, steroids, fat-
soluble vitamins, carcinogens, pesticides, and many other types of chemicals. Their catalytic …

[HTML][HTML] The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes

GCP Van Zundert, J Rodrigues, M Trellet… - Journal of molecular …, 2016 - Elsevier
The prediction of the quaternary structure of biomolecular macromolecules is of paramount
importance for fundamental understanding of cellular processes and drug design. In the era …

PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex

A Lamiable, P Thévenet, J Rey, M Vavrusa… - Nucleic acids …, 2016 - academic.oup.com
Abstract Structure determination of linear peptides of 5–50 amino acids in aqueous solution
and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel …

Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase

G Courtade, R Wimmer, ÅK Røhr… - Proceedings of the …, 2016 - National Acad Sciences
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that
catalyze oxidative cleavage of glycosidic bonds using molecular oxygen and an external …

[HTML][HTML] Deregulation of mitochondrial F1FO-ATP synthase via OSCP in Alzheimer's disease

SJ Beck, L Guo, A Phensy, J Tian, L Wang… - Nature …, 2016 - nature.com
Abstract F1FO-ATP synthase is critical for mitochondrial functions. The deregulation of this
enzyme results in dampened mitochondrial oxidative phosphorylation (OXPHOS) and …

[HTML][HTML] Engineering the surface properties of a human monoclonal antibody prevents self-association and rapid clearance in vivo

CL Dobson, PWA Devine, JJ Phillips, DR Higazi… - Scientific reports, 2016 - nature.com
Uncontrolled self-association is a major challenge in the exploitation of proteins as
therapeutics. Here we describe the development of a structural proteomics approach to …

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment

MF Lensink, S Velankar… - Proteins: Structure …, 2016 - Wiley Online Library
We present the results for CAPRI Round 30, the first joint CASP‐CAPRI experiment, which
brought together experts from the protein structure prediction and protein–protein docking …

[HTML][HTML] Spatiotemporal variation of mammalian protein complex stoichiometries

A Ori, M Iskar, K Buczak, P Kastritis, L Parca… - Genome biology, 2016 - Springer
Background Recent large-scale studies revealed cell-type specific proteomes. However,
protein complexes, the basic functional modules of a cell, have been so far mostly …

[HTML][HTML] In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules

R Ahirwar, S Nahar, S Aggarwal, S Ramachandran… - Scientific reports, 2016 - nature.com
Aptamers, the chemical-antibody substitute to conventional antibodies, are primarily
discovered through SELEX technology involving multi-round selections and enrichment …