Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
Korea Institute for Advanced Study · Radboud University Nijmegen · +4 more institutions
Abstract
A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this "last mile of the protein folding problem" and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge-based all atom force field derived from Amber, whose parameters have been optimized to minimize…
Citation impact
- FWCI
- 15.06
- Percentile
- 100%
- References
- 29
Authors
11- EKElmar KriegerCorresponding
Korea Institute for Advanced Study, Radboud University Nijmegen, University of California, Santa Cruz, University of Washington, Radboud University Medical Center
- KJKeehyoung Joo
Korea Institute for Advanced Study
- JLJinwoo Lee
Korea Institute for Advanced Study, Radboud University Nijmegen, Kwangwoon University, University of California, Santa Cruz, University of Washington, Radboud University Medical Center
- JLJinwoo LeeCorresponding
Korea Institute for Advanced Study, Radboud University Nijmegen, Kwangwoon University, University of California, Santa Cruz, University of Washington, Radboud University Medical Center
- JLJooyoung LeeCorresponding
Korea Institute for Advanced Study, Radboud University Nijmegen, Kwangwoon University, University of California, Santa Cruz, University of Washington, Radboud University Medical Center
Topics & keywords
- Computer science
- MODELLER
- Force field (fiction)
- Template
- Homology modeling
- Protein structure prediction
- Algorithm
- Protein structure