Non-sequential protein structure alignment by conformational space annealing and local refinement

Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

(2018) InSuk Joung et al.   COMPUTER PHYSICS COMMUNICATIONS

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic

(2015) Peter Brown et al.   BIOINFORMATICS

Protein structure determination by conformational space annealing using NMR geometric restraints

(2015) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational search for direct band gap silicon crystals

(2014) In-Ho Lee et al.   PHYSICAL REVIEW B

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

(2013) Shintaro Minami et al.   BMC BIOINFORMATICS

DALIX: Optimal DALI Protein Structure Alignment

(2012) Inken Wohlers et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Modularity optimization by conformational space annealing

(2012) Juyong Lee et al.   PHYSICAL REVIEW E

Biological insights from topology independent comparison of protein 3D structures

(2011) Minh N. Nguyen et al.   NUCLEIC ACIDS RESEARCH

CLICK—topology-independent comparison of biomolecular 3D structures

(2011) M. N. Nguyen et al.   NUCLEIC ACIDS RESEARCH

FlexSnap: Flexible Non-sequential Protein Structure Alignment

(2010) Saeed Salem et al.   Algorithms for Molecular Biology

A note on difficult structure alignment problems

(2008) M. J. Sippl et al.   BIOINFORMATICS

Multiple Sequence Alignment by Conformational Space Annealing

(2008) Keehyoung Joo et al.   BIOPHYSICAL JOURNAL

Novel protein folds and their nonsequential structural analogs

(2008) Aysam Guerler et al.   PROTEIN SCIENCE

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing

(2008) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS