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Academic literature on the topic 'Surface Site Interaction Points (SSIP)'
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Journal articles on the topic "Surface Site Interaction Points (SSIP)"
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Oliver, Antoni, Christopher A. Hunter, Rafel Prohens, and Josep Lluis Rosselló. "An improved methodology to compute surface site interaction points using high density molecular electrostatic potential surfaces." Journal of Computational Chemistry 39, no. 28 (2018): 2371–77. http://dx.doi.org/10.1002/jcc.25574.
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Prohens, Rafel, and Christopher A. Hunter. "Computational screens can speed up the discovery of pharmaceutical cocrystals." ADMET and DMPK 6, no. 4 (2018): 284–87. http://dx.doi.org/10.5599/admet.641.
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The calculation of Surface Site Interaction Points for cocrystal computational screens in combination with efficient experimental cocrystallization techniques has been applied successfully to several drug compounds. The basics of this combined approach are briefly reviewed in this communication.
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Nosenko, Vladimir, Aleksandr Fetisov, Sergey Nosenko, and Valeria Puzyrkova. "Morphology and Chemical Composition of Silicon Carbide Surface in Interaction with Titanium Alloy under Micro-Scratching Conditions." MATEC Web of Conferences 329 (2020): 02010. http://dx.doi.org/10.1051/matecconf/202032902010.
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The article describes features of the wear site morphology formation during micro-scratching of a titanium alloy by a silicon carbide crystal in comparison with a corundum crystal. The initial shape of the crystal top and the rate of micro-scratching were assumed to be constant. No lubricating or cooling process media were used. External factors: micro-scratch depth and cutting path length. The chemical composition of wear sites was studied using micro-x-ray spectral analysis. The content of chemical elements in the surface layer of silicon carbide and adhered metal was studied at separate points and by area scanning. The accelerating voltage of the excitation electrons was changed in the range from 5 to 20 kV. The concentration of chemical elements on the surface of the wear site was determined immediately after micro-scratching and after removing the adhered metal by etching. The regularities of changes in the concentration of chemical elements depending on the accelerating voltage of the excitation electrons were determined.
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Ge, Gang, and Jian Min Liu. "Effects of Adjacent Ground Treatment on Site Seismic Response." Applied Mechanics and Materials 90-93 (September 2011): 1576–80. http://dx.doi.org/10.4028/www.scientific.net/amm.90-93.1576.
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The effect of adjacent soil improvement on ground motion is studied using finite element method, when seismic wave is introduced from the single layer on bedrock. The influence of ground motion on soil reinforcement is analyzed; the impacts of the reinforcement zone width, depth, elastic modulus, and the soil improvement interval on response of the ground motion are also investigated. Study shows: for the same site, when the distance between two adjacent foundation consolidation interval is less than 3 to 4 times the width of the reinforcement area, the interaction acceleration response amplitude of various points on the surface of the two adjacent reinforcement area increased significantly than the single block; within the interval , increasing one of the two adjacent foundation’s width, depth, and the other foundation surface, the horizontal acceleration response will Subsequently enlarged; when the interval between the reinforcement area is greater than the range, this effect is negligible.
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Harman, Christine, Lilin Zhong, Li Ma, et al. "A View of the E2-CD81 Interface at the Binding Site of a Neutralizing Antibody against Hepatitis C Virus." Journal of Virology 89, no. 1 (2014): 492–501. http://dx.doi.org/10.1128/jvi.01661-14.
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ABSTRACTHepatitis C virus (HCV) glycoprotein E2 is considered a major target for generating neutralizing antibodies against HCV, primarily due to its role of engaging host entry factors, such as CD81, a key cell surface protein associated with HCV entry. Based on a series of biochemical analyses in combination with molecular docking, we present a description of a potential binding interface formed between the E2 protein and CD81. The virus side of this interface includes a hydrophobic helix motif comprised of residues W437LAGLF442, which encompasses the binding site of a neutralizing monoclonal antibody, mAb41. The helical conformation of this motif provides a structural framework for the positioning of residues F442 and Y443, serving as contact points for the interaction with CD81. The cell side of this interface likewise involves a surface-exposed hydrophobic helix, namely, the D-helix of CD81, which coincides with the binding site of 1D6, a monoclonal anti-CD81 antibody known to block HCV entry. Our illustration of this virus-host interface suggests an important role played by the W437LAGLF442helix of the E2 protein in the hydrophobic interaction with the D-helix of CD81, thereby facilitating our understanding of the mechanism for antibody-mediated neutralization of HCV.IMPORTANCECharacterization of the interface established between a virus and host cells can provide important information that may be used for the control of virus infections. The interface that enables hepatitis C virus (HCV) to infect human liver cells has not been well understood because of the number of cell surface proteins, factors, and conditions found to be associated with the infection process. Based on a series of biochemical analyses in combination with molecular docking, we present such an interface, consisting of two hydrophobic helical structures, from the HCV E2 surface glycoprotein and the CD81 protein, a major host cell receptor recognized by all HCV strains. Our study reveals the critical role played by hydrophobic interactions in the formation of this virus-host interface, thereby contributing to our understanding of the mechanism for antibody-mediated neutralization of HCV.
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Pandey, Vishnudatt, Gargi Tiwari, and Rajendra Prasad Ojha. "A Comparative Study of Binding of Different Drugs on gp120: Insight from Molecular Dynamics Simulation Study." Oriental Journal of Chemistry 34, no. 6 (2018): 2954–62. http://dx.doi.org/10.13005/ojc/340635.
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HIV-I cellular infection triggered by CD4 receptor protein and viral envelop glycoprotein gp120 binding event. CD4:gp120 surface is directed by the contact points of a hydrophobic gp120 cavity capped by Phe43CD4 and ionic bonds residues Arg59CD4 and Asp368gp120. The binding sites originated by gp120 and CD4 interaction leads to the entry of HIV-I into the host membrane, where, gp120 and a CD4 binding site becomes the main mark for plenty of drug uncovering program. Here, we took the crystal structure of small-molecule of gp120 in a complex that concurrently pursues both of the hotspots of gp120 binding sites. All ligands in our study are small molecules that are able to obstruct the protein-protein interactions between CD4 and gp120. This study aims at the thermodynamical insights of the ligand binding in CD4 binding sites using Molecular Dynamics Simulations Study and calculation of binding free energy. The physical of binding of drugs distinctly indicates a hydrophobic and electrostatics interaction motivated binding of ligands which explicitly mark CD4 binding sites.
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Wu, X. R., and T. T. Sun. "Molecular cloning of a 47 kDa tissue-specific and differentiation-dependent urothelial cell surface glycoprotein." Journal of Cell Science 106, no. 1 (1993): 31–43. http://dx.doi.org/10.1242/jcs.106.1.31.
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Despite the fact that bladder epithelium has many interesting biological features and is a frequent site of carcinoma formation, relatively little is known about its biochemical differentiation. We have shown recently that a 47 kDa glycoprotein, uroplakin III (UPIII), in conjunction with uroplakins I (27 kDa) and II (15 kDa), forms the asymmetric unit membrane (AUM)--a highly specialized biomembrane characteristic of the apical surface of bladder epithelium. Deglycosylation and cDNA sequencing revealed that UPIII contains up to 20 kDa of N-linked sugars attached to a core protein of 28.9 kDa. The presence of an N-terminal signal peptide sequence and a single transmembrane domain located near the C terminus, plus the N-terminal location of all the potential N-glycosylation sites, points to a type I (N-exo/C-cyto) configuration. Thus the mass of the extracellular domain (20 kDa plus up to 20 kDa of sugar) of UPIII greatly exceeds that of its intracellular domain (5 kDa). Such an asymmetrical mass distribution, a feature shared by the other two major uroplakins, provides a molecular explanation as to why the luminal leaflet of AUM is almost twice as thick as the cytoplasmic one. The fact that of the three major proteins of AUM only UPIII has a significant cytoplasmic domain suggests that this molecule may play an important role in AUM-cytoskeleton interaction in terminally differentiated urothelial cells.
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Aray, Yosslen, and Jesús Rodríguez. "Study of NO and CO dissociation on the (100) Cu surface using density functional theory and the topological analysis of the electronic density and its Laplacian." Canadian Journal of Chemistry 74, no. 6 (1996): 1014–20. http://dx.doi.org/10.1139/v96-114.
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Molecular orbital ab initio Hartree–Fock, post-Hartree–Fock at the MP2 and QCISD levels, and density functional theory calculations of the dipole moment, the topology of the electronic density, ρ(r), and its Laplacian, [Formula: see text], for CO and NO molecules are reported. The results obtained confirm that density functional methods provide remarkably good electronic properties and a good description of the topology of ρ(r) and [Formula: see text]. The Becke exchange functional with the correlation functional of Lee, Yang, and Parr was used to calculate the electronic density of the (100) Cu surface. Topological analysis of ρ(r) shows that the crystal graph corresponds to square pyramids between the atoms of the top of the surface and the atoms of the second layer The topological analysis of [Formula: see text] shows that the atomic graph of the Cu surface exhibits one (3,−3) local charge concentration surrounded by four (3,+1) local charge depletion points. Additionally, there is a (3,+3) local depletion in the midpoint between each of four contiguous Cu atoms corresponding to the active site for the adsorption of the (3,−3) local charge concentration on the C atom of the CO or the N atom of the NO molecule. The larger value of the [Formula: see text] at the nonbonded charge concentration on the atoms and the geometrical configuration of these critical points favor the interaction of the NO over the CO molecule with the (100) Cu surface. This result is in accord with the known reaction barriers for these molecules. Key words: density functional theory, Laplacian of the electronic density, (100) Cu surface, carbon monoxide, nitrogen monoxide, molecular graph, atomic graph.
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Zeigler, K. E., P. Hogan, C. Hughes, and A. Kurota. "Native American lithic procurement along the international border in the boot heel region of southwestern New Mexico." Solid Earth 2, no. 1 (2011): 75–93. http://dx.doi.org/10.5194/se-2-75-2011.
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Abstract. Multidisciplinary field projects can be very useful to a more fundamental understanding of the world around us, though these projects are not as common as they should be. In particular, the combination of archeology and geology combines our understanding of human behavior and human use of the landscape with an intimate knowledge of geologic processes and the materials available for human use in order to gain a broader understanding of human-Earth interaction. Here we present data from a cross-disciplinary project that uses a common dataset, archeological artifacts, to explore the anthropological and geologic implications of useage patterns. Archeological excavations and surveys conducted by the Office of Contract Archeology in 2007 along the route of the proposed international border fence reveal patterns of use of geologic materials by Archaic, Formative and Protohistoric Native Americans in the Boot Heel of southwestern New Mexico. Thousands of artifacts were recorded in multiple sites from Guadalupe Pass in the southern Peloncillo Mountains to the Carrizalillo Hills west of Columbus. We identified the lithologies of artifacts, ranging from projectile points to groundstones, and then constructed material movement maps based on either known procurement sites ("quarries") or outcrops identified as the closest source to a given site for each lithology. Not unexpectedly, the majority of the rock types utilized by native peoples are local siliceous volcanic materials. However, several artifacts constructed from obsidian were transported into the region from northern Mexico and eastern Arizona, indicating long-distance travel and/or trade routes. We also examine useage pattern difference between Archaic, Formative and Protohistoric sites. Additionally, a dramatic change in distribution of sources for geologic materials occurs between one pre-Spanish site and one post-Spanish site that are adjacent to one another.
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Didier, Andrea, Richard Dietrich, Stephanie Gruber, et al. "Monoclonal Antibodies Neutralize Bacillus cereus Nhe Enterotoxin by Inhibiting Ordered Binding of Its Three Exoprotein Components." Infection and Immunity 80, no. 2 (2011): 832–38. http://dx.doi.org/10.1128/iai.05681-11.
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ABSTRACTThe Nhe enterotoxin fromBacillus cereusis known to induce cytotoxicity on Vero and CaCo-2 cells by ordered binding of its single components NheA, NheB, and NheC. This study aimed to elucidate functional sites on NheB by identifying the epitopes of the neutralizing monoclonal antibodies 1E11 and 2B11. The binding regions of both antibodies were determined by using recombinant NheB fragments and synthetic peptides. The antigenic site of antibody 1E11 was located within the amino acids 321 to 341 of NheB, whereas reactivity of antibody 2B11 was dependent on the presence of amino acids 122 to 150 and on conformation. Both antibodies were able to bind simultaneously to NheB and did not interfere with target cell binding as shown by immunofluorescence microscopy. A set of neutralization assays revealed that antibody 2B11 most likely interfered with the interaction between NheB and NheC both on the epithelium cell surface and in solution. In contrast, antibody 1E11 inhibited association between NheA and cell-bound NheB in a competitive manner, and effectively neutralized Nhe cytotoxicity on a variety of human cell lines. This distinct mechanism further supports that NheA is the key component during the Nhe mode of action and the C-terminal epitope recognized by antibody 1E11 points to an important functional region of NheB.
Dissertations / Theses on the topic "Surface Site Interaction Points (SSIP)"
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Oliver, Gelabert Antoni. "Desarrollo y aceleración hardware de metodologías de descripción y comparación de compuestos orgánicos." Doctoral thesis, Universitat de les Illes Balears, 2018. http://hdl.handle.net/10803/462902.
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Introducción
El acelerado ritmo al que se genera y crece la información en la sociedad actual y la posible llegada de la tecnología de transistor a sus límites de tamaño exige la puesta en marcha de soluciones para el procesado eficiente de datos en campos específicos de aplicación.
Contenido
Esta tesis doctoral de carácter transdisciplinar a medio camino entre la ingeniería electrónica y la química computacional presenta soluciones optimizadas en hardware y en software para la construcción y el procesado eficiente de bases de datos moleculares.
En primer lugar se propone y se estudia el funcionamiento de bloques digitales que implementan funciones en lógica pulsante estocástica orientadas a tareas de reconocimiento de objetos. Especialmente se proponen y analizan diseños digitales para la construcción de generadores de números aleatorios (RNG) como base de estos sistemas que han sido implementados en dispositivos Field Programable Gate Array (FPGA).
En segundo lugar se propone y se evalúa un conjunto reducido de descriptores moleculares para la caracterización de compuestos orgánicos y la generación de bases de datos moleculares. Estos descriptores recogen información sobre la distribución de la carga molecular en el espacio y la energía electrostática. Las bases de datos generadas con estos descriptores se han procesado utilizando sistemas de computación convencionales en software y mediante sistemas de computación estocástica implementados en hardware mediante el uso de circuitería digital programable.
Finalmente se proponen optimizaciones para la estimación del potencial electrostático molecular (MEP) y para el cálculo de los puntos de interacción molecular derivados (SSIP).
Conclusiones
Por una parte, los resultados obtenidos ponen de manifiesto la importancia de la uniformidad de los RNG en el período de evaluación para poder implementar sistemas de computación estocástica de alta fiabilidad. Además, los RNG propuestos tienen una naturaleza aperiódica que minimiza las posibles correlaciones entre señales, haciendo que sean adecuados para la implementación de sistemas de computación estocástica.
Por otra parte, el conjunto de descriptores moleculares propuestos PED han demostrado obtener muy buenos resultados en comparación con otros métodos presentes en la literatura. Este hecho se ha discutido mediante los parámetros Area Under The Curve (AUC) y Enrichment Factor (EF) obtenidos de las curvas promedio Receiving Operating Characteristic (ROC). Además, se ha mostrado como la eficacia de los descriptores aumenta cuando se implementan en sistemas de clasificación con aprendizaje supervisado, haciéndolos adecuados para la construcción de un sistema de predicción de dianas terapéuticas eficiente.
En esta tesis, además, se ha determinado que los MEP calculados utilizando la teoría DFT y el conjunto de bases B3LYP/6-31*G en la superficie con densidad electrónica 0,01 au correlacionan bien con datos experimentales debido presumiblemente a la mayor contribución de las propiedades electrostáticas locales reflejadas en el MEP. Las parametrizaciones propuestas en función del tipo de hibridación atómica pueden haber contribuido también a esta mejora. Los cálculos realizados en dichas superficies suponen mejoras en un factor cinco en la velocidad de procesamiento del MEP.
Dado el aceptable ajuste a datos experimentales del método propuesto para el cálculo del MEP aproximado y de los SSIP, éste se puede utilizar con el fin de obtener los SSIP para bases de datos moleculares extensas o en macromoléculas como proteínas de manera muy rápida (ya que la velocidad de procesamiento obtenida puede alcanzar del orden de cinco mil átomos procesados por segundo utilizando un solo procesador).
Estas técnicas resultan de especial interés dadas las numerosas aplicaciones de los SSIP como por ejemplo el cribado virtual de cocristales o la predicción de energías libres en disolución.<br>Introducció
El creixement accelerat de les dades en la societat actual i l'arribada de la tecnologia del transistor als límits físics exigeix la proposta de metodologies per al processament eficient de dades.
Contingut
Aquesta tesi doctoral, de caràcter transdisciplinària i a mig camí entre els camps de l'enginyeria electrònica i la química computacional presenta solucions optimitzades en maquinari i en programari per tal d’accelerar el processament de bases de dades moleculars.
En primer lloc es proposa i s'estudia el funcionament de blocs digitals que implementen funcions de lògica polsant estocàstica aplicades a tasques de reconeixement d'objectes. En concret es proposen i analitzen dissenys específics per a la construcció de generadors de nombres aleatoris (RNG) com a sistemes bàsics per al funcionament dels sistemes de computació estocàstics implementats en dispositius programables com les Field Programable Gate Array (FPGA).
En segon lloc es proposen i avaluen un conjunt reduït de descriptors moleculars especialment orientats a la caracterització de compostos orgànics. Aquests descriptors reuneixen la informació sobre la distribució de càrrega molecular i les energies electroestàtiques. Les bases de dades generades amb aquests descriptors s’han processat emprant sistemes de computació convencionals en programari i mitjançant sistemes basats en computació estocàstica implementats en maquinari programable.
Finalment es proposen optimitzacions per al càlcul del potencial electroestàtic molecular (MEP) calculat mitjançant la teoria del funcional de la densitat (DFT) i dels punts d’interacció que se’n deriven (SSIP).
Conclusions
Per una banda, els resultats obtinguts posen de manifest la importància de la uniformitat del RNG en el període d’avaluació per a poder implementar sistemes de computació estocàstics d’alta fiabilitat. A més, els RNG proposats presenten una font d’aleatorietat aperiòdica que minimitza les correlacions entre senyals, fent-los adequats per a la implementació de sistemes de computació estocàstica.
Per una altra banda, el conjunt de descriptors moleculars proposats PED, han demostrat obtenir molts bons resultats en comparació amb els mètodes presents a la literatura. Aquest fet ha estat discutit mitjançant l’anàlisi dels paràmetres Area Under The Curve (AUC) i Enrichment Factor (EF) de les curves Receiving Operating Characteristic (ROC) analitzades. A més, s’ha mostrat com l’eficàcia dels descriptors augmenta de manera significativa quan s’implementen en sistemes de classificació amb aprenentatge supervisat com les finestres de Parzen, fent-los adequats per a la construcció d’un sistema de predicció de dianes terapèutiques eficient.
En aquesta tesi doctoral, a més, s’ha trobat que els MEP calculats mitjançant la teoria DFT i el conjunt de bases B3LYP/6-31*G en la superfície amb densitat electrònica 0,01 au correlacionen bé amb dades experimentals possiblement a causa de la contribució més gran de les propietats electroestàtiques locals reflectides en el MEP. Les parametritzacions proposades en funció del tipus d’hibridació atòmica han contribuït també a la millora dels resultats. Els càlculs realitzats en aquestes superfícies suposen un guany en un factor cinc en la velocitat de processament del MEP.
Donat l’acceptable ajust a les dades experimentals del mètode proposat per al càlcul del MEP aproximat i dels SSIP que se’n deriven, aquest procediment es pot emprar per obtenir els SSIP en bases de dades moleculars extenses i en macromolècules (com ara proteïnes) d’una manera molt ràpida (ja que la velocitat de processament obtinguda arriba fins als cinc mil àtoms per segon amb un sol processador).
Les tècniques proposades en aquesta tesi doctoral resulten d’interès donades les nombroses aplicacions que tenen els SSIP com per exemple, en el cribratge virtual de cocristalls o en la predicció d’energies lliures en dissolució.<br>Introduction
Because of the generalized data growth in the nowadays digital era and due to the fact that we are possibly living on the last days of the Moore’s law, there exists a good reason for being focused on the development of technical solutions for efficient data processing.
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In this transdisciplinary thesis between electronic engineering and computational chemistry, it's shown optimal solutions in hardware and software for molecular database processing.
On the first hand, there's proposed and studied a set of stochastic computing systems in order to implement ultrafast pattern recognition applications. Specially, it’s proposed and analyzed specific digital designs in order to create digital Random Number Generators (RNG) as a base for stochastic functions. The digital platform used to generate the results is a Field Programmable Gate Array (FPGA).
On the second hand, there's proposed and evaluated a set of molecular descriptors in order to create a compact molecular database. The proposed descriptors gather charge and molecular geometry information and they have been used as a database both in software conventional computing and in hardware stochastic computing.
Finally, there's a proposed a set of optimizations for Molecular Electrostatic Potential (MEP) and Surface Site Interaction Points (SSIP).
Conclusions
Firstly, the results show the relevance of the uniformity of the RNG within the evaluation period in order to implement high precision stochastic computing systems. In addition, the proposed RNG have an aperiodic behavior which avoid some potential correlations between stochastic signals. This property makes the proposed RNG suitable for implementation of stochastic computing systems.
Secondly, the proposed molecular descriptors PED have demonstrated to provide good results in comparison with other methods that are present in the literature. This has been discussed by the use of Area Under the Curve (AUC) and Enrichment Factor (EF) of averaged Receiving Operating Characteristic (ROC) curves. Furthermore, the performance of the proposed descriptors gets increased when they are implemented in supervised machine learning algorithms making them appropriate for therapeutic target predictions.
Thirdly, the efficient molecular database characterization and the usage of stochastic computing circuitry can be used together in order to implement ultrafast information processing systems.
On the other hand, in this thesis, it has been found that the MEP calculated by using DFT and B3LYP/6-31*G basis at 0.01 au density surface level has good correlation with experimental data. This fact may be due to the important contribution of local electrostatics and the refinement performed by the parameterization of the MEP as a function of the orbital atom type. Additionally, the proposed calculation over 0.01 au is five times faster than the calculation over 0.002 au.
Finally, due to acceptable agreement between experimental data and theoretical results obtained by using the proposed calculation for MEP and SSIP, the proposed method is suitable for being applied in order to quickly process big molecular databases and macromolecules (the processing speed can achieve five thousand molecules per second using a single processor).
The proposed techniques have special interest with the purpose of finding the SSIP because the big number of applications they have as for instance in virtual cocrystal screening and calculation of free energies in solution.