Algorithm 1 Vina-GPU method

Input: random ligand conformations: $\left\{{\mathbf{C}}_{{tmp}_0},{\mathbf{C}}_{{tmp}_1},\dots ,{\mathbf{C}}_{{tmp}_N}\right\}$

Output: top k ligand conformations $\left\{{\mathbf{C}}_0,{\mathbf{C}}_1,\dots ,{\mathbf{C}}_{k-1}\right\}\in \left\{{\mathbf{C}}_{{tmp}_0},{\mathbf{C}}_{{tmp}_1},\dots ,{\mathbf{C}}_{{tmp}_N}\right\}$

1: for all ${\mathbf{C}}_{tm{p}_i}\left(i=0,1,\dots ,N\right)$ concurrently do   2:  for all $search\_depth=0,1,2,\cdots ,r$ do   3:    ${\mathbf{C}}_{{cand}_i}=Mutation\left({\mathbf{C}}_{{tmp}_i}\right)$   4:    $\left({\mathbf{C}}_{{cand}_i},e_{can{d}_i}\right)=BFGS\left({\mathbf{C}}_{{cand}_i}\right)\&Scoring\left({\mathbf{C}}_{{cand}_i}\right)$   5:   if $search\_depth==0\Vert Metropolis\left(e_{can{d}_i},e_{tm{p}_i}\right)$ then   6:    ${\mathbf{C}}_{{tmp}_i}={\mathbf{C}}_{{cand}_i}$   7:     $\left({\mathbf{C}}_{{cand}_i},e_{can{d}_i}\right)=BFGS\left({\mathbf{C}}_{{tmp}_i}\right)\&Scoring\left({\mathbf{C}}_{{tmp}_i}\right)$   8:   end if   9:  end for 10: end for 11: $Clustering\&Sorting({\mathbf{C}}_{{tmp}_0},{\mathbf{C}}_{{tmp}_1},\dots ,{\mathbf{C}}_{{tmp}_N})$ 12: return $\left\{{\mathbf{C}}_0,{\mathbf{C}}_1,\dots ,{\mathbf{C}}_{k-1}\right\}\in \left\{{\mathbf{C}}_{{tmp}_0},{\mathbf{C}}_{{tmp}_1},\dots ,{\mathbf{C}}_{{tmp}_N}\right\}$