Efficiency of tabu‐search‐based conformational search algorithms

Abstract

Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings.

Helicusin E, Isochromophilone X and Isochromophilone XI: New Chloroazaphilones Produced by the Fungus Bartalinia robillardoides Strain LF550

“…Consequently H-4 and H-3′/H-9 have to be located on opposite sides of the lactone-ring plane, leaving only the two enantiomers with the 3 S ,7 R ,9 R - and 3 R ,7 S ,9 S -configuration as possible stereoisomers. Starting from the minimum structure found with CAST [19], a conformational analysis of the S , R , R -configuration using B97-D/TZVP gave only twelve structures within an energetic range of 3 kcal/mol. Single-point calculations with SCS-MP2/def2-TZVP and COSMO (methanol) reduced this number of possible conformations to six.…”

“…The conformational analyses of the two diastereomers of 6 were started with CAST [19] using the OPLS_AA forcefield [24] with subsequent PM7 optimizations using MOPAC2012 [25]. From the thus found lowest conformations a more in-depth analysis was performed using B97-D/TZVP [26,27] within Gaussian09 [28].…”

TANGO: A high through‐put conformation generation and semiempirical method‐based optimization tool for ligand molecules

“…A holistic view of the methods designed to achieve conformation generation suggests that they either follow a stochastic or a systematic approach . The stochastic methods are the ones that perform conformational search based on molecular dynamics (MD) and Monte Carlo (MC) techniques . However, this sampling is followed by scoring of the conformations generated using techniques like distance geometry and genetic algorithm.…”

Gradient gravitational search: An efficient metaheuristic algorithm for global optimization

“…A good combination between intensification and diversification ensures the selection of the best solutions to improve the rate of algorithm convergence and its global optimality. [20] Metaheuristic optimization algorithms include the ability to reach a problems global minimum value at an early with a reduce number of control parameters at low computational cost, as well as robustness and wide application to several different problems based on Chemistry and Physics, [21][22][23][24][25][26] based on Engineering Design. [27][28][29][30][31][32][33][34][35][36][37][38][39] It is also quite evident that algorithms may not exactly fit into the mentioned requisites efficiently.…”