101
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Nasonov AF. Computational methods and software in computer-aided combinatorial library design. RUSS J GEN CHEM+ 2011. [DOI: 10.1134/s1070363210120248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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102
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Huang SY, Grinter SZ, Zou X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 2010; 12:12899-908. [PMID: 20730182 PMCID: PMC11103779 DOI: 10.1039/c0cp00151a] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are used for protein-ligand docking. The commonly-used assessment criteria and publicly available protein-ligand databases for performance evaluation of the scoring functions have also been presented and discussed. We end with a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions.
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
| | - Sam Z. Grinter
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
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103
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Sheridan RP, Maiorov VN, Holloway MK, Cornell WD, Gao YD. Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. J Chem Inf Model 2010; 50:2029-40. [PMID: 20977231 DOI: 10.1021/ci100312t] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One approach to estimating the "chemical tractability" of a candidate protein target where we know the atomic resolution structure is to examine the physical properties of potential binding sites. A number of other workers have addressed this issue. We characterize ~290,000 "pockets" from ~42,000 protein crystal structures in terms of a three parameter "pocket space": volume, buriedness, and hydrophobicity. A metric DLID (drug-like density) measures how likely a pocket is to bind a drug-like molecule. This is calculated from the count of other pockets in its local neighborhood in pocket space that contain drug-like cocrystallized ligands and the count of total pockets in the neighborhood. Surprisingly, despite being defined locally, a global trend in DLID can be predicted by a simple linear regression on log(volume), buriedness, and hydrophobicity. Two levels of simplification are necessary to relate the DLID of individual pockets to "targets": taking the best DLID per Protein Data Bank (PDB) entry (because any given crystal structure can have many pockets), and taking the median DLID over all PDB entries for the same target (because different crystal structures of the same protein can vary because of artifacts and real conformational changes). We can show that median DLIDs for targets that are detectably homologous in sequence are reasonably similar and that median DLIDs correlate with the "druggability" estimate of Cheng et al. (Nature Biotechnology 2007, 25, 71-75).
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Affiliation(s)
- Robert P Sheridan
- Chemistry Modeling and Informatics Department, Merck Research Laboratories, Rahway, New Jersey 07065, USA.
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104
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Jain AN. QMOD: physically meaningful QSAR. J Comput Aided Mol Des 2010; 24:865-78. [PMID: 20721601 DOI: 10.1007/s10822-010-9379-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 08/03/2010] [Indexed: 10/19/2022]
Abstract
Computational methods for predicting ligand affinity where no protein structure is known generally take the form of regression analysis based on molecular features that have only a tangential relationship to a protein/ligand binding event. Such methods have utility in retrospective rationalization of activity patterns of substituents on a common scaffold, but are limited when either multiple scaffolds are present or when ligand alignment varies significantly based on structural changes. In addition, such methods generally assume independence and additivity of effect from scaffold substituents. Collectively, these non-physical modeling assumptions sharply limit the utility of widely used QSAR approaches for prospective prediction of ligand activity. The recently introduced Surflex-QMOD approach, by virtue of constructing physical models of binding sites, comes closer to a modeling approach that is congruent with protein ligand binding events. A set of congeneric CDK2 inhibitors showed that induced binding pockets can be quite congruent with the enzyme's active site but that model predictivity within a chemical series does not necessarily depend on congruence. Muscarinic antagonists were used to show that the QMOD approach is capable of making accurate predictions in cases where highly non-additive structure activity effects exist. The QMOD method offers a means to go beyond non-causative correlations in QSAR analysis.
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Affiliation(s)
- Ajay N Jain
- Department of Bioengineering and Therapeutic Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, 1450 3rd Street, Room D373, MC 0128, P.O. Box 589001, San Francisco, CA 94158-9001, USA.
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105
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Abstract
In this paper we provide an overview of our current knowledge of the mapping between small molecule ligands and protein domains. We give an overview of the present data resources available on the Web, which provide information about protein-ligand interactions, as well as discussing our own PROCOGNATE database. We present an update of ligand binding in large protein superfamilies and identify those ligands most frequently utilized by nature. Finally we discuss potential uses for this type of data.
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Affiliation(s)
- Matthew Bashton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
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106
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Hinz U. From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci 2010; 67:1049-64. [PMID: 20043185 PMCID: PMC2835715 DOI: 10.1007/s00018-009-0229-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/01/2009] [Accepted: 12/07/2009] [Indexed: 11/12/2022]
Abstract
With the dramatic increase in the volume of experimental results in every domain of life sciences, assembling pertinent data and combining information from different fields has become a challenge. Information is dispersed over numerous specialized databases and is presented in many different formats. Rapid access to experiment-based information about well-characterized proteins helps predict the function of uncharacterized proteins identified by large-scale sequencing. In this context, universal knowledgebases play essential roles in providing access to data from complementary types of experiments and serving as hubs with cross-references to many specialized databases. This review outlines how the value of experimental data is optimized by combining high-quality protein sequences with complementary experimental results, including information derived from protein 3D-structures, using as an example the UniProt knowledgebase (UniProtKB) and the tools and links provided on its website ( http://www.uniprot.org/ ). It also evokes precautions that are necessary for successful predictions and extrapolations.
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Affiliation(s)
- Ursula Hinz
- Swiss-Prot Group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211, Geneva, Switzerland.
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107
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Zhou P, Zou J, Tian F, Shang Z. Fluorine Bonding — How Does It Work In Protein−Ligand Interactions? J Chem Inf Model 2009; 49:2344-55. [DOI: 10.1021/ci9002393] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Jianwei Zou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Feifei Tian
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Zhicai Shang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
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109
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Lee S, Brown A, Pitt WR, Higueruelo AP, Gong S, Bickerton GR, Schreyer A, Tanramluk D, Baylay A, Blundell TL. Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics. MOLECULAR BIOSYSTEMS 2009; 5:1456-72. [DOI: 10.1039/b906402h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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110
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Bauer RA, Günther S, Jansen D, Heeger C, Thaben PF, Preissner R. SuperSite: dictionary of metabolite and drug binding sites in proteins. Nucleic Acids Res 2008; 37:D195-200. [PMID: 18842629 PMCID: PMC2686477 DOI: 10.1093/nar/gkn618] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increasing structural information about target-bound compounds provide a rich basis to study the binding mechanisms of metabolites and drugs. SuperSite is a database, which combines the structural information with various tools for the analysis of molecular recognition. The main data is made up of 8000 metabolites including 1300 drugs, bound to about 290 000 different receptor binding sites. The analysis tools include features, like the highlighting of evolutionary conserved receptor residues, the marking of putative binding pockets and the superpositioning of different binding sites of the same ligand. User-defined compounds can be edited or uploaded and will be superimposed with the most similar co-crystallized ligand. The user can examine all results online with the molecule viewer Jmol. An implemented search algorithm allows the screening of uploaded proteins, in order to detect potential drug binding sites, which are similar to known binding pockets. The huge data set of target-bound compounds in combination with the provided analysis tools allow to inspect the characteristics of molecular recognition, especially for drug target interactions. SuperSite is publicly available at: http://bioinformatics.charite.de/supersite.
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Affiliation(s)
- Raphael André Bauer
- Institute of Molecular Biology and Bioinformatics, Structural Bioinformatics Group, Charité- Medical University Berlin, Arnimallee 22, 14195 Berlin, Germany
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