Predicting protein–protein interactions from the molecular to the proteome level
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 …
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in …
CD Putnam, M Hammel, GL Hura… - Quarterly reviews of …, 2007 - cambridge.org
Crystallography supplies unparalleled detail on structural information critical for mechanistic
analyses; however, it is restricted to describing low energy conformations of …
analyses; however, it is restricted to describing low energy conformations of …
PIC: protein interactions calculator
KG Tina, R Bhadra, N Srinivasan - Nucleic acids research, 2007 - academic.oup.com
Interactions within a protein structure and interactions between proteins in an assembly are
essential considerations in understanding molecular basis of stability and functions of …
essential considerations in understanding molecular basis of stability and functions of …
Predicting functionally important residues from sequence conservation
JA Capra, M Singh - Bioinformatics, 2007 - academic.oup.com
Motivation: All residues in a protein are not equally important. Some are essential for the
proper structure and function of the protein, whereas others can be readily replaced …
proper structure and function of the protein, whereas others can be readily replaced …
ProFunc: a server for predicting protein function from 3D structure
RA Laskowski, JD Watson… - Nucleic acids research, 2005 - academic.oup.com
Abstract ProFunc (http://www. ebi. ac. uk/thornton-srv/databases/ProFunc) is a web server for
predicting the likely function of proteins whose 3D structure is known but whose function is …
predicting the likely function of proteins whose 3D structure is known but whose function is …
Analysis of catalytic residues in enzyme active sites
GJ Bartlett, CT Porter, N Borkakoti… - Journal of molecular …, 2002 - Elsevier
We present an analysis of the residues directly involved in catalysis in 178 enzyme active
sites. Specific criteria were derived to define a catalytic residue, and used to create a …
sites. Specific criteria were derived to define a catalytic residue, and used to create a …
Structural analysis of B-cell epitopes in antibody: protein complexes
The binding of antigens to antibodies is one of the key events in an immune response
against foreign molecules and is a critical element of several biomedical applications …
against foreign molecules and is a critical element of several biomedical applications …
Loss of protein structure stability as a major causative factor in monogenic disease
The most common cause of monogenic disease is a single base DNA variant resulting in an
amino acid substitution. In a previous study, we observed that a high fraction of these …
amino acid substitution. In a previous study, we observed that a high fraction of these …
A dissection of specific and non-specific protein–protein interfaces
We compare the geometric and physical–chemical properties of interfaces involved in
specific and non-specific protein–protein interactions in crystal structures reported in the …
specific and non-specific protein–protein interactions in crystal structures reported in the …
3D complex: a structural classification of protein complexes
ED Levy, JB Pereira-Leal, C Chothia… - PLoS computational …, 2006 - journals.plos.org
Most of the proteins in a cell assemble into complexes to carry out their function. It is
therefore crucial to understand the physicochemical properties as well as the evolution of …
therefore crucial to understand the physicochemical properties as well as the evolution of …