225 citations · 647 across the 6 of their papers we have counts for
6 papers
Multistep greedy algorithm identifies community structure in real-world and computer-generated networks
Philipp Schuetz, Amedeo Caflisch
We have recently introduced a multistep extension of the greedy algorithm for modularity optimization. The extension is based on the idea that merging l pairs of communities (l>1)…
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement
Philipp Schuetz, Amedeo Caflisch
Identifying strongly connected substructures in large networks provides insight into their coarse-grained organization. Several approaches based on the optimization of a quality fu…
Estimation of protein folding probability from equilibrium simulations
Francesco Rao, Giovanni Settanni, Enrico Guarnera +1
The assumption that similar structures have similar folding probabilities () leads naturally to a procedure to evaluate for every snapshot saved along an equil…
Local modularity measure for network clusterizations
Stefanie Muff, Francesco Rao, Amedeo Caflisch
Many complex networks have an underlying modular structure, i.e., structural subunits (communities or clusters) characterized by highly interconnected nodes. The modularity has…
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
M. Cecchini, F. Rao, M. Seeber +1
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation spac…
The protein folding network
Francesco Rao, Amedeo Caflisch
The conformation space of a 20-residue antiparallel -sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, an…