Template-based protein structure modeling
A Fiser - Computational biology, 2010 - Springer
Functional characterization of a protein is often facilitated by its 3D structure. However, the
fraction of experimentally known 3D models is currently less than 1% due to the inherently …
fraction of experimentally known 3D models is currently less than 1% due to the inherently …
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties …
Motivation: In recent years, development of a single-method fold-recognition server lags
behind consensus and multiple template techniques. However, a good consensus …
behind consensus and multiple template techniques. However, a good consensus …
Quality assessment of protein structure models
D Kihara, H Chen, YD Yang - Current protein and peptide …, 2009 - ingentaconnect.com
Computational protein tertiary structure prediction has made significant progress over the
last decade due to the advancement of techniques and the growth of sequence and …
last decade due to the advancement of techniques and the growth of sequence and …
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model
How to recognize the structural fold of a protein is one of the challenges in protein structure
prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP2 …
prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP2 …
Quality assessment of protein model-structures using evolutionary conservation
Motivation: Programs that evaluate the quality of a protein structural model are important
both for validating the structure determination procedure and for guiding the model-building …
both for validating the structure determination procedure and for guiding the model-building …
Template-based protein modeling: recent methodological advances
Protein modeling has been a very challenging problem in drug discovery and computational
biology. The latest advances and progress in computational power have helped to solve this …
biology. The latest advances and progress in computational power have helped to solve this …
Comparative protein structure modelling
A Fiser - From protein structure to function with bioinformatics, 2017 - Springer
A prerequisite to understand cell functioning on the system level is the knowledge of three-
dimensional protein structures that mediate biochemical interactions. The explosion in the …
dimensional protein structures that mediate biochemical interactions. The explosion in the …
A point mutation in the extracellular domain of KIT promotes tumorigenesis of mastcells via ligand-independent auto-dimerization
Y Amagai, A Matsuda, K Jung, K Oida, H Jang… - Scientific Reports, 2015 - nature.com
Mutations in the juxtamembrane and tyrosine kinase domains of the KIT receptor havebeen
implicated in several cancers and are known to promote tumorigenesis. However, the …
implicated in several cancers and are known to promote tumorigenesis. However, the …
A template‐finding algorithm and a comprehensive benchmark for homology modeling of proteins
The first step in homology modeling is to identify a template protein for the target sequence.
The template structure is used in later phases of the calculation to construct an atomically …
The template structure is used in later phases of the calculation to construct an atomically …
Sub-AQUA: real-value quality assessment of protein structure models
YD Yang, P Spratt, H Chen, C Park… - … Engineering, Design & …, 2010 - academic.oup.com
Computational protein tertiary structure prediction has made significant progress over the
past years. However, most of the existing structure prediction methods are not equipped with …
past years. However, most of the existing structure prediction methods are not equipped with …