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Chareshneu A, Pant P, Tristão Ramos RJ, Sehnal D, Gökbel T, Ionescu CM, Koča J. NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors. ACS OMEGA 2021; 6:23023-23027. [PMID: 34549102 PMCID: PMC8444218 DOI: 10.1021/acsomega.1c00817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) comprise a large and ancient family of allosteric ion channels mediating synaptic transmission. The vast knowledge about nAChRs has become difficult to navigate. NAChRDB is a web-accessible resource of curated residue-level functional annotations of neuromuscular nAChRs. Interactive three-dimensional (3D) visualization and sequence alignment give further context to this rich and growing collection of experimental observations and computational predictions. NAChRDB is freely available at https://crocodile.ncbr.muni.cz/Apps/NAChRDB/, with interactive tutorials and regular updates to the content and web interface. No installation or user registration is required. NAChRDB is accessible through any modern internet browser on desktops and mobile devices. By providing immediate and systematic access to practical knowledge gained through decades of research, NAChRDB represents a powerful educational tool and helps guide discovery by revealing gaps in current knowledge and aiding the interpretation of results of molecular and structural biology experiments or computational studies.
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Affiliation(s)
- Aliaksei Chareshneu
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Purbaj Pant
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Ravi José Tristão Ramos
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - David Sehnal
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Protein
Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.
| | - Tuğrul Gökbel
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, İzmir 35430, Turkey
| | - Crina-Maria Ionescu
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Jaroslav Koča
- CEITEC
- Central European Institute of Technology, Masaryk University, Brno 601 77, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
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2
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Dashnaw CM, Koone JC, Abdolvahabi A, Shaw BF. Measuring how two proteins affect each other's net charge in a crowded environment. Protein Sci 2021; 30:1594-1605. [PMID: 33928693 DOI: 10.1002/pro.4092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = -0.43 ± 0.01) and α-lactalbumin (Zmonomer = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Zdimer = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
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Affiliation(s)
- Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Alireza Abdolvahabi
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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3
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Raček T, Schindler O, Toušek D, Horský V, Berka K, Koča J, Svobodová R. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res 2020; 48:W591-W596. [PMID: 32402071 PMCID: PMC7319571 DOI: 10.1093/nar/gkaa367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/16/2022] Open
Abstract
Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.
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Affiliation(s)
- Tomáš Raček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic.,Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Ondřej Schindler
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Dominik Toušek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Vladimír Horský
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc 771 46, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Radka Svobodová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
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4
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Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. Biomolecules 2020; 10:biom10091308. [PMID: 32932757 PMCID: PMC7564285 DOI: 10.3390/biom10091308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 01/07/2023] Open
Abstract
Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 μs) of the murine γ-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.
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Shaimardanov AR, Shulga DA, Palyulin VA. Iterative Solvers for Empirical Partial Atomic Charges: Breaking the Curse of Cubic Numerical Complexity. J Chem Inf Model 2019; 59:1434-1443. [PMID: 30883114 DOI: 10.1021/acs.jcim.8b00848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rational drug design involves a vast amount of computations to get thermodynamically reliable results and often relies on atomic charges as a means to model electrostatic interactions within the system. Computational inefficiency often hampers the development of new and wider dissemination of the known methods; thus, any source to speed up the calculations without a sacrifice in quality is warranted. At the heart of many empirical methods of calculating atomic charges is the solution of a system of linear algebraic equations (SLAE). The classical method of solving SLAE-the Gauss method-has in general case a cubic computational complexity. It is shown that the use of iterative methods for solving SLAE, characteristic to typical empirical atomic charge calculation methods, makes it possible to significantly reduce the amount of calculations and to obtain a computational complexity approaching a quadratic one. Despite the fact that this phenomenon is well-known in numerical methods, iterative solvers surprisingly do not seem to have been systematically applied to calculation of atomic charges via empirical schemes. Another finding is the relative values of the matrix elements, determined by the physical grounds of the interactions within the empirical system, generally lead to SLAE's with well-defined matrices, suited to use with iterative solvers to fasten computation compared to using the noniterative solvers. This finding broadens the applicability range of atomic charges obtained with empirical methods for such cases as, e.g., account of polarizability via "on-the-fly" recalculation of charges in changing surroundings within the force fields in molecular dynamics settings.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry , Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry , Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry , Lomonosov Moscow State University , Moscow 119991 , Russian Federation
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Maurya SR, Mahalakshmi R. Mitochondrial VDAC2 and cell homeostasis: highlighting hidden structural features and unique functionalities. Biol Rev Camb Philos Soc 2016; 92:1843-1858. [PMID: 28980434 DOI: 10.1111/brv.12311] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Abstract
Voltage-dependent anion channels (VDACs) are the gateway to mitochondrial processes, interlinking the cytosolic and mitochondrial compartments. The mitochondrion acts as a storehouse for cytochrome c, the effector of apoptosis, and hence VDACs become intricately involved in the apoptotic pathway. Isoform 1 of VDAC is abundant in the outer mitochondrial membrane of many cell types, while isoform 2 is the preferred channel in specialized cells including brain and some cancer cells. The primary role of VDACs is metabolite flux. The pro- and anti-apoptotic role of VDAC1 and VDAC2, respectively, are secondary, and are influenced by external factors and interacting proteins. Herein, we focus on the less-studied VDAC2, and shed light on its unique functions and features. VDAC2, along with sharing many of its functions with VDAC1, such as metabolite and Ca2+ transport, also has many delineating functions. VDAC2 is closely engaged in the gametogenesis and steroidogenesis pathways and in protection from oxidative stress as well as in neurodegenerative diseases like Alzheimer's and epilepsy. A closer examination of the functional pathways of VDACs indicates that the unique functions of VDAC2 are a result of the different interactome of this isoform. We couple functional differences to the structural and biophysical evidence obtained for the VDACs, and present a testament of why the two VDAC isoforms with >90% sequence similarity, are functionally diverse. Based on these differences, we suggest that the VDAC isoforms now be considered as paralogs. An in-depth understanding of VDAC2 will help us to design better biomolecule targets for cancer and neurodegenerative diseases.
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Affiliation(s)
- Svetlana Rajkumar Maurya
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India
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Affiliation(s)
- Zhenyan Jiang
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
| | - Hansi Zhang
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
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AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J Cheminform 2015; 7:50. [PMID: 26500704 PMCID: PMC4613891 DOI: 10.1186/s13321-015-0099-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
Background Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. Results This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical
method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Conclusions Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.
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Lindner AU, Prehn JHM, Huber HJ. The indirect activation model of mitochondrial outer membrane permeabilisation (MOMP) initiation requires a trade-off between robustness in the absence of and sensitivity in the presence of stress. MOLECULAR BIOSYSTEMS 2014; 9:2359-69. [PMID: 23824068 DOI: 10.1039/c3mb70076c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondrial outer membrane permeabilisation (MOMP) is a hallmark of apoptosis and is controlled by antagonising members of the BCL 2 protein family. However, whether the effector proteins for MOMP, BAX and BAK, require a separate activation step (direct activation model) or if the sole inhibition of otherwise active effectors by anti-apoptotic BCL 2 proteins suffices (indirect activation model) is controversial. To address this question, we recently identified that, in most cells, effector proteins were more abundant than their inhibitors. We now employ systems modelling to elucidate fundamental consequences of this imbalance for the indirect activation model by integrating its key features into the recently validated implementation of the direct activation model. First, by modelling constitutively active BAK, several cell lines were predicted to be unstable against MOMP even in the absence of stress. This instability could be rectified by assuming BAK pores to be subject to degradation, which however demanded BAK to underlie a high and biologically unreasonable protein turnover. Stability against MOMP in the absence of stress was similarly reconstituted by assuming BAK oligomerisation to be weak, but predicted some cells to be MOMP resistant even under high stress. Assuming also BAX to be constitutively active required highly effective BAX re-translocation to the cytosol along with weak BAX oligomerisation, which again rendered some cells insensitive to induce MOMP in the presence of stress. Our results suggest that an activation step of the two effectors is required to allow stability against MOMP in the absence of stress and execution of MOMP under stress.
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Affiliation(s)
- Andreas U Lindner
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons, 123 St. Stephens Green, Dublin 2, Ireland
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10
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Geidl S, Ionescu CM, Vařeková RS, Koča J. QM quality atomic charges for proteins. J Cheminform 2014. [PMCID: PMC3980139 DOI: 10.1186/1758-2946-6-s1-p61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. J Chem Theory Comput 2013; 9:4684-4691. [PMID: 24634618 PMCID: PMC3948463 DOI: 10.1021/ct400514p] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Indexed: 11/29/2022]
Abstract
![]()
The
accelerated molecular dynamics (aMD) method has recently been shown
to enhance the sampling of biomolecules in molecular dynamics (MD)
simulations, often by several orders of magnitude. Here, we describe
an implementation of the aMD method for the OpenMM application layer
that takes full advantage of graphics processing units (GPUs) computing.
The aMD method is shown to work in combination with the AMOEBA polarizable
force field (AMOEBA-aMD), allowing the simulation of long time-scale
events with a polarizable force field. Benchmarks are provided to
show that the AMOEBA-aMD method is efficiently implemented and produces
accurate results in its standard parametrization. For the BPTI protein,
we demonstrate that the protein structure described with AMOEBA remains
stable even on the extended time scales accessed at high levels of
accelerations. For the DNA repair metalloenzyme endonuclease IV, we
show that the use of the AMOEBA force field is a significant improvement
over fixed charged models for describing the enzyme active-site. The
new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that
can benefit from both the use of a polarizable force field and enhanced
sampling.
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Affiliation(s)
- Steffen Lindert
- Department of Pharmacology, University of California San Diego , La Jolla, California 92093 United States ; Center for Theoretical Biological Physics, La Jolla, California 92093 United States
| | - Denis Bucher
- Howard Hughes Medical Institute, University of California San Diego , La Jolla, California 92093 United States ; Department of Chemistry & Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego , La Jolla, California 92093, United States
| | - Peter Eastman
- Department of Bioengineering, Stanford University , Stanford, California 94305, United States
| | - Vijay Pande
- Department of Bioengineering, Stanford University , Stanford, California 94305, United States
| | - J Andrew McCammon
- Department of Pharmacology, University of California San Diego , La Jolla, California 92093 United States ; Center for Theoretical Biological Physics, La Jolla, California 92093 United States ; Howard Hughes Medical Institute, University of California San Diego , La Jolla, California 92093 United States ; Department of Chemistry & Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego , La Jolla, California 92093, United States
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Ionescu CM, Geidl S, Svobodová Vařeková R, Koča J. Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J Chem Inf Model 2013; 53:2548-58. [DOI: 10.1021/ci400448n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Crina-Maria Ionescu
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Stanislav Geidl
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Jaroslav Koča
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
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Pramanik M, Chatterjee N, Das S, Saha KD, Bhaumik A. Anthracene-bisphosphonate based novel fluorescent organic nanoparticles explored as apoptosis inducers of cancer cells. Chem Commun (Camb) 2013; 49:9461-3. [DOI: 10.1039/c3cc44989k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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