ArticleJournal of molecular modeling2016
MOLS 2.0: software package for peptide modeling and protein-ligand docking.
Article in Journal of molecular modeling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Open-Source Machine Learning in Computational Chemistry.Journal of chemical information and modeling · 2023Review
- Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process.Molecules (Basel, Switzerland) · 2022Review
- EmbedDTI: Enhancing the Molecular Representations via Sequence Embedding and Graph Convolutional Network for the Prediction of Drug-Target Interaction.Biomolecules · 2021Article
- Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute.International journal of molecular sciences · 2020Review
- DeepBindRG: a deep learning based method for estimating effective protein-ligand affinity.PeerJ · 2019Article
- Protein-small molecule docking with receptor flexibility in iMOLSDOCK.Journal of computer-aided molecular design · 2018Article
- Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design.Frontiers in pharmacology · 2018Review
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Authors and funding
2 authors.
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Abstract
We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (MOLS) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted MOLS 1.0. The docking portion of the algorithm, which allows only "flexible ligand/rigid receptor" docking, was denoted MOLSDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for MOLS 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating "induced fit" side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed MOLS 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of MOLS 2.0. The source code and binary for MOLS 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .
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