Structure-based strategies for drug design and discovery

ID Kuntz - Science, 1992 - science.org
Most drugs have been discovered in random screens or by exploiting information about
macromolecular receptors. One source of this information is in the structures of critical …

Bacterial ribonucleases and their roles in RNA metabolism

DH Bechhofer, MP Deutscher - Critical reviews in biochemistry and …, 2019 - Taylor & Francis
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent
years, there has been a surge of new information about RNases and the roles they play in …

Very fast empirical prediction and rationalization of protein pKa values

H Li, AD Robertson, JH Jensen - Proteins: Structure, Function …, 2005 - Wiley Online Library
A very fast empirical method is presented for structure‐based protein pKa prediction and
rationalization. The desolvation effects and intra‐protein interactions, which cause variations …

Structural basis of perturbed pKa values of catalytic groups in enzyme active sites

TK Harris, GJ Turner - IUBMB life, 2002 - Wiley Online Library
In protein and RNA macromolecules, only a limited number of different side‐chain chemical
groups are available to function as catalysts. The myriad of enzyme‐catalyzed reactions …

Development of force field parameters for the simulation of single-and double-stranded DNA molecules and DNA–protein complexes

MR Tucker, S Piana, D Tan, MV LeVine… - The Journal of …, 2022 - ACS Publications
Although molecular dynamics (MD) simulations have been used extensively to study the
structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based …

Backbone Dynamics ofEscherichia coliRibonuclease HI: Correlations with Structure and Function in an Active Enzyme

AM Mandel, M Akke, AG Palmer III - Journal of molecular biology, 1995 - Elsevier
Ribonuclease H is an endonuclease that hydrolyzes the RNA moiety of RNA–DNA duplex
molecules. Escherichia coliribonuclease H is involved in DNA replication, and retroviral …

Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases

F Dyda, AB Hickman, TM Jenkins, A Engelman… - Science, 1994 - science.org
HIV integrase is the enzyme responsible for inserting the viral DNA into the host
chromosome; it is essential for HIV replication. The crystal structure of the catalytically active …

Two‐metal ion catalysis in enzymatic Acyl‐and phosphoryl‐transfer reactions

N Sträter, WN Lipscomb, T Klabunde… - … International Edition in …, 1996 - Wiley Online Library
Numerous studies, both in enzymatic and nonenzymatic catalysis, have been undertaken to
understand the way by which metal ions, especially zinc ions, promote the hydrolysis of …

Enhanced genome annotation using structural profiles in the program 3D-PSSM

LA Kelley, RM MacCallum, MJE Sternberg - Journal of molecular biology, 2000 - Elsevier
A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise
remote protein sequence homologues is described. The method combines the power of …

Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG

AE Sauer-Eriksson, GJ Kleywegt, M Uhlén, TA Jones - Structure, 1995 - cell.com
Background: Streptococcal protein G comprises two or three domains that bind to the
constant Fc region of most mammalian immunoglobulin Gs (IgGs). Protein G is functionally …