Docking screens for novel ligands conferring new biology: Miniperspective

JJ Irwin, BK Shoichet - Journal of medicinal chemistry, 2016 - ACS Publications
It is now plausible to dock libraries of 10 million molecules against targets over several days
or weeks. When the molecules screened are commercially available, they may be rapidly …

[HTML][HTML] Homology modeling a fast tool for drug discovery: current perspectives

VK Vyas, RD Ukawala, M Ghate… - Indian journal of …, 2012 - ncbi.nlm.nih.gov
Major goal of structural biology involve formation of protein-ligand complexes; in which the
protein molecules act energetically in the course of binding. Therefore, perceptive of protein …

Atlas of the radical SAM superfamily: divergent evolution of function using a “plug and play” domain

GL Holliday, E Akiva, EC Meng, SD Brown… - Methods in …, 2018 - Elsevier
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a
remarkably broad range of reactions required for life, including metabolism, nucleic acid …

Assessment of template based protein structure predictions in CASP9

V Mariani, F Kiefer, T Schmidt, J Haas… - Proteins: Structure …, 2011 - Wiley Online Library
Abstract In the Ninth Edition of the Critical Assessment of Techniques for Protein Structure
Prediction (CASP9), 61,665 models submitted by 176 groups were assessed for their …

The enzyme function initiative

JA Gerlt, KN Allen, SC Almo, RN Armstrong… - Biochemistry, 2011 - ACS Publications
The Enzyme Function Initiative (EFI) was recently established to address the challenge of
assigning reliable functions to enzymes discovered in bacterial genome projects; in this …

Divergent evolution in enolase superfamily: strategies for assigning functions

JA Gerlt, PC Babbitt, MP Jacobson, SC Almo - Journal of Biological …, 2012 - ASBMB
Nature's strategies for evolving catalytic functions can be deciphered from the information
contained in the rapidly expanding protein sequence databases. However, the functions of …

Molecular docking screens using comparative models of proteins

H Fan, JJ Irwin, BM Webb, G Klebe… - Journal of chemical …, 2009 - ACS Publications
Two orders of magnitude more protein sequences can be modeled by comparative
modeling than have been determined by X-ray crystallography and NMR spectroscopy …

[HTML][HTML] Outcome of a workshop on applications of protein models in biomedical research

T Schwede, A Sali, B Honig, M Levitt, HM Berman… - Structure, 2009 - cell.com
We describe the proceedings and conclusions from the" Workshop on Applications of
Protein Models in Biomedical Research"(the Workshop) that was held at the University of …

Molecular modeling and ligand docking for solute carrier (SLC) transporters

A Schlessinger, N Khuri… - Current topics in …, 2013 - ingentaconnect.com
Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as
ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy …

[PDF][PDF] Connecting Unexplored Protein Crystal Structures to Enzymatic Function.

F Steffen‐Munsberg, C Vickers, A Thontowi… - …, 2013 - academia.edu
Biocatalysis has emerged as an important alternative to traditional chemical synthesis for the
preparation of fine chemicals,[1] as recently demonstrated by the biocatalytic manufacture of …