In silico methods and tools for drug discovery
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …
develop new drugs, but the process from lead identification to clinical trials takes more than …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations
Structure prediction for proteins lacking homologous templates in the Protein Data Bank
(PDB) remains a significant unsolved problem. We developed a protocol, CI-TASSER, to …
(PDB) remains a significant unsolved problem. We developed a protocol, CI-TASSER, to …
GalaxyRefine: Protein structure refinement driven by side-chain repacking
The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …
methods strongly depends on the degree of similarity between the target and available …
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field
Ab initio protein folding is one of the major unsolved problems in computational biology
owing to the difficulties in force field design and conformational search. We developed a …
owing to the difficulties in force field design and conformational search. We developed a …
Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
Protein structure prediction from sequence variation
Genomic sequences contain rich evolutionary information about functional constraints on
macromolecules such as proteins. This information can be efficiently mined to detect …
macromolecules such as proteins. This information can be efficiently mined to detect …
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …
helical and sheet conformations for protein polypeptide backbone even before the first …
Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions
Sequence-based contact prediction has shown considerable promise in assisting non-
homologous structure modeling, but it often requires many homologous sequences and a …
homologous structure modeling, but it often requires many homologous sequences and a …
Crystal structure of a monomeric retroviral protease solved by protein folding game players
Following the failure of a wide range of attempts to solve the crystal structure of M-PMV
retroviral protease by molecular replacement, we challenged players of the protein folding …
retroviral protease by molecular replacement, we challenged players of the protein folding …