Matthew C. Lee, Jinxia Deng, James M. Briggs, Yong Duan
Keywords: molecular dynamics; HIV-1 Integrase; locally enhanced sampling; structure-function
"This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at
The rough energy landscapes and tight packing of protein interiors are two of the critical factors that have prevented the wide application of physics-based models in protein side-chain assignment...
The rough energy landscapes and tight packing of protein interiors are two of the critical factors that have prevented the wide application of physics-based models in protein side-chain assignment...
The rough energy landscapes and tight packing of protein interiors are two of the critical factors that have prevented the wide application of physics-based models in protein side-chain assignment...
Matthew C. Lee, Jinxia Deng, Y James M. Briggs, Yong Duan
ABSTRACT HIV-1 integrase is one of the three essential enzymes required for viral replication and has great potential as a novel target for anti-HIV drugs. Although tremendous efforts have been...
Incorporating intermolecular distance into protein-protein docking (2005)
In this work, intermolecular distance was integrated into the docking of protein-protein complexes. To develop an efficient docking procedure, 22 enzyme-inhibitor targets and 15 antibody-antigen...
Incorporating intermolecular distance into protein-protein docking (2004)
In this work, intermolecular distance was integrated into the docking of protein–protein complexes. To develop an efficient docking procedure, 22 enzyme–inhibitor targets and 15...
Duan, Yong, Wang, Lu, Kollman, Peter A.
A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of...
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
Chong, Lillian T., Duan, Yong, Wang, Lu, Massova, Irina, Kollman, Peter A.
We investigated the relative free energies of hapten binding to the germ line and mature forms of the 48G7 antibody Fab fragments by applying a continuum model to structures sampled from molecular...
Wu, Chun, Lei, Hongxing, Duan, Yong
A combined total of more than 600.0 ns molecular dynamics simulations with explicit solvent have been carried on systems containing either four peptides or a single peptide to investigate the...
Multiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes†
Fischer, Amanda J., Rockwell, Nathan C., Jang, Abigail Y., Ernst, Lauren A., Waggoner, Alan S., Duan, Yong, ...
The phytochrome family of red/far-red photoreceptors has been optimized to support photochemical isomerization of a bound bilin chromophore, a process that triggers a conformational change and...
Wu, Chun, Lei, Hongxing, Duan, Yong
We observed fast aggregation of partially ordered oligomers in an earlier simulation study of an amyloidogenic hexapeptide NFGAIL. In this work, the nucleation of highly ordered oligomers was further...
Lee, Matthew C., Deng, Jinxia, Briggs, James M., Duan, Yong
HIV-1 integrase is one of the three essential enzymes required for viral replication and has great potential as a novel target for anti-HIV drugs. Although tremendous efforts have been devoted to...
Yang, Rong, Lee, Matthew C., Yan, Honggao, Duan, Yong
Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding...
Duan, Yong, Wang, Lu, Kollman, Peter A.
A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of...
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
Chong, Lillian T., Duan, Yong, Wang, Lu, Massova, Irina, Kollman, Peter A.
We investigated the relative free energies of hapten binding to the germ line and mature forms of the 48G7 antibody Fab fragments by applying a continuum model to structures sampled from molecular...
Wu, Chun, Lei, Hongxing, Duan, Yong
A combined total of more than 600.0 ns molecular dynamics simulations with explicit solvent have been carried on systems containing either four peptides or a single peptide to investigate the...
Wu, Chun, Lei, Hongxing, Duan, Yong
We observed fast aggregation of partially ordered oligomers in an earlier simulation study of an amyloidogenic hexapeptide NFGAIL. In this work, the nucleation of highly ordered oligomers was further...
Lee, Matthew C., Deng, Jinxia, Briggs, James M., Duan, Yong
HIV-1 integrase is one of the three essential enzymes required for viral replication and has great potential as a novel target for anti-HIV drugs. Although tremendous efforts have been devoted to...
Yang, Rong, Lee, Matthew C., Yan, Honggao, Duan, Yong
Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding...
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
Lei, Hongxing, Wu, Chun, Liu, Haiguang, Duan, Yong
High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica...
Wu, Chun, Lei, Hongxing, Wang, Zhixiang, Zhang, Wei, Duan, Yong
Amyloid-associated diseases affect millions of people worldwide. Phenol red exhibits modest inhibition toward fibril formation of human Islet amyloid polypeptide (hIAPP) and its toxicity, which is...
Lei, Hongxing, Wu, Chun, Wang, Zhi-Xiang, Zhou, Yaoqi, Duan, Yong
Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding...
The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier
Lei, Hongxing, Deng, Xiaojian, Wang, Zhixiang, Duan, Yong
The LYS24∕29NLE double mutant of villin headpiece subdomain (HP35) is the fastest folding protein known so far with a folding time constant of 0.6 μs. In this work, the folding mechanism of the...