Methods such as Principal Component Analysishave been used in funnel visualization for isobutyryl-3-NH-methyl, where disconnectivity graphs were used to visualize the overall organization of the landscape. The potential energy surface is represented in terms of local minima and the transition states that connect them, providing a convenient coarse-grained representation of the corresponding landscape. This method has been applied to a wide number of systems. For Clofentezine example, Lennard-Jones clusters present multi-funnel characteristics. Disconnectivity graphs are able to reveal the effects of gatekeepers in the potential energy surface by raising the energies of low-lying minima relative to the global minimum. The diferences in folding efficiencies can also be inferred in proteins with and without frustration for structure based models. Disconnectivity graphs can also be extended for the visualization of free energy landscape, maintaining the description of barriers faithfully. When rate constants are associated with the rearrangements mediated by each transition state, a kinetic transition network can be defined. So the kinetics and thermodynamics of complex transitions can be modeled in terms of transitions between the relevant conformational substates, in which kinetic transition networks are constructed from geometry optimization and molecular dynamics simulations. These examples show that this method overcomes the fundamental limitations of reactioncoordinate-based methods. Most of these approaches emphasize the kinetic path between probed states, and are able to indicate, for example, the funnel aspect of the landscape against a hub-like hypothesis. In this paper we focus on the Pancuronium dibromide structural organization of conformations, looking at the difference of contacts in each conformation. We propose a suitable conformation metric that reflects the underlying landscape in which the kinetics takes place. The method is tested in a 27-mer protein lattice model, folded into a36363 cube, which has been extensively used in protein folding studies, and in particular for visualization methods. We restricted the visualization to local minima of regions from around the transition-state to the native state. These partially folded states are the relevant ones in the study of metastable states and function-related conformation changes. The data obtained from computational simulations in a lattice model were projected on a 2D or 3D plot with the Force-Scheme method, which allowed us to map the connectivity of conformations. The choice of a metric is essential in order to reach a sensible connection between the original data and the projection, and it must efficiently distinguish between pairs of conformations. From the analyses, we noted that distinct sequences lead to different patterns, from which folding routes could be established and the effects from mutations could be probed. The latter can be probed by analyzing the folding routes, for in a good funnel representation the folding route has to be represented by a sequence of small steps in the 
effective funnel representation. Figure 4a shows two routes generated from first passage time simulations, which show mostly small steps between successive minima. The details of this representation can be seen in different folding routes, which probe very distinct regions of the phase space. Also worth mentioning is that the routes do not directly cross the empty regions, but go around them through neighboring connected states.