Vibrational spectroscopic detection of beta-and gamma-turns in synthetic and natural peptides and proteins
The final goal of functional genomics is to determine the biological role for all of the genes in
a cell. At present, the genome-scale prediction of protein function is based primarily on the …
a cell. At present, the genome-scale prediction of protein function is based primarily on the …
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
A novel energy model (VSGB 2.0) for high resolution protein structure modeling is
described, which features an optimized implicit solvent model as well as physics‐based …
described, which features an optimized implicit solvent model as well as physics‐based …
A hierarchical approach to all‐atom protein loop prediction
MP Jacobson, DL Pincus, CS Rapp… - Proteins: Structure …, 2004 - Wiley Online Library
The application of all‐atom force fields (and explicit or implicit solvent models) to protein
homology‐modeling tasks such as side‐chain and loop prediction remains challenging both …
homology‐modeling tasks such as side‐chain and loop prediction remains challenging both …
Recent developments in structural proteomics for protein structure determination
HL Liu, JP Hsu - Proteomics, 2005 - Wiley Online Library
The major challenges in structural proteomics include identifying all the proteins on the
genome‐wide scale, determining their structure‐function relationships, and outlining the …
genome‐wide scale, determining their structure‐function relationships, and outlining the …
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction
In this paper, we introduce a method to account for the shape of the potential energy curve in
the evaluation of conformational free energies. The method is based on a procedure that …
the evaluation of conformational free energies. The method is based on a procedure that …
Modeling structurally variable regions in homologous proteins with rosetta
A major limitation of current comparative modeling methods is the accuracy with which
regions that are structurally divergent from homologues of known structure can be modeled …
regions that are structurally divergent from homologues of known structure can be modeled …
PROFcon: novel prediction of long-range contacts
Motivation: Despite the continuing advance in the experimental determination of protein
structures, the gap between the number of known protein sequences and structures …
structures, the gap between the number of known protein sequences and structures …
Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential
The conformations of loops are determined by the water‐mediated interactions between
amino acid residues. Energy functions that describe the interactions can be derived either …
amino acid residues. Energy functions that describe the interactions can be derived either …
Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling
YA Arnautova, RA Abagyan… - … : Structure, Function, and …, 2011 - Wiley Online Library
We report the development of internal coordinate mechanics force field (ICMFF), new force
field parameterized using a combination of experimental data for crystals of small molecules …
field parameterized using a combination of experimental data for crystals of small molecules …
Protein backbone angle prediction with machine learning approaches
Motivation: Protein backbone torsion angle prediction provides useful local structural
information that goes beyond conventional three-state (α, β and coil) secondary structure …
information that goes beyond conventional three-state (α, β and coil) secondary structure …