• Publications
  • Influence
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
TLDR
It is concluded that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. Expand
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
TLDR
An efficient way to make a random step in a Monte Carlo procedure given knowledge of the energy or statistical properties of conformational subspaces is found, and the BPMC procedure is applied to the structure prediction of 12- and 16-residue synthetic peptides and the determination of protein structure from NMR data. Expand
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes*
TLDR
A new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites is developed and the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified. Expand
Docking and scoring with ICM: the benchmarking results and strategies for improvement
TLDR
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set and significant improvements up to ROC AUC = 82.2 and ROC(2%) =–45.2 were achieved following best practices for flexible pocket refinement and out-of-pocket binding rescore. Expand
Flexible protein–ligand docking by global energy optimization in internal coordinates
TLDR
Eight protein–ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side‐chain entropy in the internal coordinate space of the flexible ligand and the receptor side chains by using two types of efficient random moves. Expand
Flexible ligand docking to multiple receptor conformations: a practical alternative.
TLDR
Here it is shown that using multiple fixed receptor conformations, either experimentally determined by crystallography or NMR, or computationally generated, is a practical shortcut that may improve docking calculations. Expand
Discovery of a Cyclic Boronic Acid β-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases.
TLDR
Studies in vitro and in vivo show that RPX7009 (9f) is a broad-spectrum inhibitor, notably restoring the activity of carbapenems against KPC-producing strains, and 9f is a promising product for the treatment of multidrug resistant Gram-negative bacteria. Expand
Soft protein–protein docking in internal coordinates
TLDR
An efficient pseudo‐Brownian rigid‐body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side‐chains is presented and can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. Expand
PIER: Protein interface recognition for structural proteomics
TLDR
An improved method for predicting interfaces from a single protein structure, which is based on local statistical properties of the protein surface derived at the level of atomic groups, which makes PIER a suitable tool for automated high‐throughput annotation of protein structures emerging from structural proteomics projects. Expand
Comparative study of several algorithms for flexible ligand docking
TLDR
ICM provided the highest accuracy in ligand docking against these receptors, and was able to identify the original ligands within the top 1% of the total library in 17 cases. Expand
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