Verenluovuttajien rekisteritiedon hyödyntäminen ja kontaktoinnin kehittäminen CRM-järjestelmän avulla

Diplomityön tavoitteena on kartoittaa Suomen Punaisen Ristin Veripalvelun verenluovutustoiminnan luovuttajahallinnan nyky- ja tavoitetilaa haastattelujen, havainnoinnin sekä dokumentaation perusteella. Kartoituksen ja kuiluanalyysin avulla voidaan arvioida Microsoftin asiakassuhteiden hallintaan tarkoitetun järjestelmän soveltuvuutta Veripalvelun käyttöön. Lisäksi arvioidaan strategisen CRM-viitekehyksen soveltamista Veripalvelun luovuttajasuhteiden hallintaan, joka tarjoaa kokonaisvaltaisen ja poikkifunktionaalisen näkemyksen kriittisiin prosesseihin ja aktiviteetteihin. Asiakassuhteiden hallinta pitää nähdä kokonaisvaltaisena, koko organisaatiota koskevana jatkuvan kehittämisen kohteena olevana toimintona joka tuo lisäarvoa sekä organisaatiolle itselleen että sen asiakkaille. Voittoa tavoittelemattoman organisaation toimintaympäristössä Veripalvelulla ei ole suoraa kilpailua, joka on otettava huomioon luovuttajasuhteiden hallinnassa. Tulevaisuuden tavoitteet kartoittamalla voi kohdeorganisaatio huomioida strategisesti tärkeä osa-alueet, jotka takaavat kilpailukyvyn ja mahdollistavat arvonluonnin asiakasprosesseissa.

Study of the shelf-life of a mixed araça (Psidium guineensis Sw.) and marolo (Annona crassiflora Mart.) jam

The objective of this study was to add value to araça and marolo fruits by developing jams and verifying changes in their physical, chemical, and microbiological parameters during storage. The analyses were carried out every 2 months. From the results, it was shown that the levels of moisture (35.89 - 26.34%), lipids (0.43 - 0.27%), sucrose (30.62 - 28.98%), total pectin (0.83 - 0.50%), soluble pectin (0.52 - 0.38%), total phenolic compounds (180.31 - 135.52 mg.GAE 100 g-1), and organic acids (401.1 - 68.5 µg.g-1 citric acid) decreased during storage. However, the levels of protein (0.83 - 0.95%), carbohydrate (62.52 - 72.5%, calories (257,11 - 295,931 kcal), fiber (0.72 - 1.4%), total soluble sugar (62.52 - 70.44%), reducing sugar (32.05 - 41.41%), soluble solids (68.4 - 72.18 °Brix), consistency (0.33 - 0.44 N), total antioxidant potential (11.3 - 22.63%), and color (a* 7.56 - 9.49, and b* 8.63 - 10.49) increased during 1-year storage. The quality of the fruit jams studied was in accordance with the microbiological standards established by the Brazilian legislation. It was concluded that the mixed araça and marolo jam can be stored for 1 year without the addition of additives.

Stability of cassava flour-based food bars

The consumption of Brazilian cassava has been reduced due to a lack of adjustment to the modern lifestyle. To reverse this trend, new products could be developed specifically targeted to high-value niche markets. Cereal bars stand out as fast food high in nutritional value. A bar formula mimicking cereal bars was prepared using a mixture of Brazilian cassava flour, hydrogenated vegetable fat, dried bananas, ground cashew nuts, and glucose syrup. After being pressed, the bars were dried for 1 hour at 65 °C, packaged in films, and stored under ambient conditions. Its stability was continuously monitored for 210 days in order to ensure its safety and enable its introduction to the market. Texture loss was observed in the packed bars after 90 days of storage, but the sensory characteristics allowed the testers to perceive this tendency after only 30 days of storage. However, chemical, physical, and microbial analyses confirmed that the bars were safe for consumption for 180 days. The results showed that a 45 g cassava flour-based bar enriched with nuts and dried fruits can meet 6% of the recommended daily fiber intake with a caloric value between that of the common cereal bar and that of an energy bar. Adapting the formula with ingredients (fruits, nuts) from different regions of Brazil may add value to this traditional product as a fast food.

Stability of gluten free sweet biscuit elaborated with rice bran, broken rice and okara

Abstract A challenge to the food sector has been the development of new products incorporating co-products from the food processing industry with minimal impact on their pre-determined structures and adding nutritional quality. In order to add value and develop alternatives for the use of co-products generated during the agroindustrial processing, this work aimed to study the stability of gluten-free sweet biscuits developed with soybean okara, rice bran and broken rice. The formulations were elaborated with increasing percentages of these ingredients and compared with the standard (commercial sweet biscuit) for ten months. The analyses were: weight, diameters (internal and external), thickness, specific volume, instrumental parameters of color, texture, scanning electron microscopy, water activity, proximal composition and isoflavones. The experimental sweet biscuits had characteristics of color, weight, volume and diameters (internal and external) very similar to the commercial, whereas texture, lipids and energy value decreased, and aw, moisture and protein increased during storage. The sweet biscuits showed the same stability when compared to the standard, and the

Location intelligence strategisen päätöksenteon tukena

Kilpailuetua tavoittelevan yrityksen pitää kyetä jalostamaan tietoa ja tunnistamaan sen avulla uusia tulevaisuuden mahdollisuuksia. Tulevaisuuden mielikuvien luomiseksi yrityksen on tunnettava toimintaympäristönsä ja olla herkkänä havaitsemaan muutostrendit ja muut toimintaympäristön signaalit. Ympäristön elintärkeät signaalit liittyvät kilpailijoihin, teknologian kehittymiseen, arvomaailman muutoksiin, globaaleihin väestötrendeihin tai jopa ympäristön muutoksiin. Spatiaaliset suhteet ovat peruspilareita käsitteellistää maailmaamme. Pitney (2015) on arvioinut, että 80 % kaikesta bisnesdatasta sisältää jollakin tavoin viittauksia paikkatietoon. Siitä huolimatta paikkatietoa on vielä huonosti hyödynnetty yritysten strategisten päätösten tukena. Teknologioiden kehittyminen, tiedon nopea siirto ja paikannustekniikoiden integroiminen eri laitteisiin ovat mahdollistaneet sen, että paikkatietoa hyödyntäviä palveluja ja ratkaisuja tullaan yhä enemmän näkemään yrityskentässä. Tutkimuksen tavoitteena oli selvittää voiko location intelligence toimia strategisen päätöksenteon tukena ja jos voi, niin miten. Työ toteutettiin konstruktiivista tutkimusmenetelmää käyttäen, jolla pyritään ratkaisemaan jokin relevantti ongelma. Konstruktiivinen tutkimus tehtiin tiiviissä yhteistyössä kolmen pk-yrityksen kanssa ja siihen haastateltiin kuutta eri strategiasta vastaavaa henkilöä. Tutkimuksen tuloksena löydettiin, että location intelligenceä voidaan hyödyntää strategisen päätöksenteon tukena usealla eri tasolla. Yksinkertaisimmassa karttaratkaisussa halutut tiedot tuodaan kartalle ja luodaan visuaalinen esitys, jonka avulla johtopäätöksien tekeminen helpottuu. Toisen tason karttaratkaisu pitää sisällään sekä sijainti- että ominaisuustietoa, jota on yhdistetty eri lähteistä. Tämä toisen tason karttaratkaisu on usein kuvailevaa analytiikkaa, joka mahdollistaa erilaisten ilmiöiden analysoinnin. Kolmannen eli ylimmän tason karttaratkaisu tarjoaa ennakoivaa analytiikkaa ja malleja tulevaisuudesta. Tällöin ohjelmaan koodataan älykkyyttä, jossa informaation keskinäisiä suhteita on määritelty joko tiedon louhintaa tai tilastollisia analyysejä hyödyntäen. Tutkimuksen johtopäätöksenä voidaan todeta, että location intelligence pystyy tarjoamaan lisäarvoa strategisen päätöksenteon tueksi, mikäli yritykselle on hyödyllistä ymmärtää eri ilmiöiden, asiakastarpeiden, kilpailijoiden ja markkinamuutoksien maantieteellisiä eroavaisuuksia. Parhaimmillaan location intelligence -ratkaisu tarjoaa luotettavan analyysin, jossa tieto välittyy muuttumattomana päätöksentekijältä toiselle ja johtopäätökseen johtaneita syitä on mahdollista palata tarkastelemaan tarvittaessa uudelleen.

Alkoholin verkkokauppamarkkinat Suomessa

Opinnäytetyö alkoholin verkkokauppamarkkinoista Suomessa on katsaus markkinoihin, jotka ovat olleet esillä mediassa viime aikoina hyvinkin paljon. Opinnäytetyössä analysoidaan Michael Porterin viiden kilpailuvoiman mallin avulla toimialaa. Porterin viisi kilpailuvoimaa ovat toimialan nykyinen kilpailu, tavarantoimittajien neuvotteluvoima, kuluttajien neuvotteluvoima, uusien kilpailijoiden uhka sekä korvaavien tuotteiden tai palveuluiden uhka. Tämän lisäksi työssä tarkastellaan lainsäädäntöä kuudentena kilpailuvoimana, sillä se asettaa merkittävät kilpailulliset reunaehdot. Toimiala-analyysin jälkeen siirrytään varsinaiseen tutkimusongelmaan, jossa pohditaan, kannattaako Alkon perustaa verkkokauppa? Tähän liittyen apututkimuskysymyksissä pohditaan mitä lisäarvoa alkoholin verkkokauppa luo ylipäätään kuluttajille sekä tavarantoimittajille/maahantuojille. Opinnäytetyöhön on liitetty ajatuksia, joita on kerätty haastattelemalla kolmea eri henkilöä, joilta löytyy merkittävästi tietoa alkoholimarkkinoista. Alko Oy ei ole osallisena, vaan opinnäytetyö on kirjoitettu täysin objektiivisesti, vaikka siinä onkin paljon kirjoittan omaa empiriaa. Haastattelut ovat tarkoituksella jätetty keskustelunomaisiksi, ja ovat siten melko subjektiivisia näkemyksiä eri ihmisten silmin. Monopolit herättävät keskustelua ja Alkon asema yhteiskunnallisena monopolina onkin asetettu kriittiseen tarkasteluun tutkimuksessa. Teoriassa käsiteltiin myös Alkon palvelualttiutta 4C –mallin avulla sekä Alkoa yrityksenä analysoitiin SWOT –analyysilla. Näiden teorioiden, toimiala-analyysin, haastatteluiden, kirjoittajan oman näkemyksen sekä eri lähteistä löydetyn informaation myötä voidaan todeta, että Alkon verkkokaupalle on tarve, joka on ollut olemassa jo pitkään. Monopoliaseman oletetaan olleen syy tälle hitaalle kehitykselle. Kuluttajien lisäarvoa olisi ehdottomasti kotiinkuljetus, mutta sitä Alko ei tarjoa. Toisaalta verkkokaupan myötä laajeneva tuotevalikoima on selkeä lisäarvo. Tavarantoimittajien/maahantuojien lisäarvoa ei vielä pystytty selvittämään, koska siihen suhtauduttiin ristiriitaisesti.

Dynamic Performance Evaluation of Canadian Fixed-Income Funds using Markov Regime Switching Models

This thesis examines the performance of Canadian fixed-income mutual funds in the context of an unobservable market factor that affects mutual fund returns. We use various selection and timing models augmented with univariate and multivariate regime-switching structures. These models assume a joint distribution of an unobservable latent variable and fund returns. The fund sample comprises six Canadian value-weighted portfolios with different investing objectives from 1980 to 2011. These are the Canadian fixed-income funds, the Canadian inflation protected fixed-income funds, the Canadian long-term fixed-income funds, the Canadian money market funds, the Canadian short-term fixed-income funds and the high yield fixed-income funds. We find strong evidence that more than one state variable is necessary to explain the dynamics of the returns on Canadian fixed-income funds. For instance, Canadian fixed-income funds clearly show that there are two regimes that can be identified with a turning point during the mid-eighties. This structural break corresponds to an increase in the Canadian bond index from its low values in the early 1980s to its current high values. Other fixed-income funds results show latent state variables that mimic the behaviour of the general economic activity. Generally, we report that Canadian bond fund alphas are negative. In other words, fund managers do not add value through their selection abilities. We find evidence that Canadian fixed-income fund portfolio managers are successful market timers who shift portfolio weights between risky and riskless financial assets according to expected market conditions. Conversely, Canadian inflation protected funds, Canadian long-term fixed-income funds and Canadian money market funds have no market timing ability. We conclude that these managers generally do not have positive performance by actively managing their portfolios. We also report that the Canadian fixed-income fund portfolios perform asymmetrically under different economic regimes. In particular, these portfolio managers demonstrate poorer selection skills during recessions. Finally, we demonstrate that the multivariate regime-switching model is superior to univariate models given the dynamic market conditions and the correlation between fund portfolios.

La culture comme ressource : des groupes musicaux populaires au sein du processus de réaménagement urbain à Rio de Janeiro

Ce projet de maîtrise porte sur l’interaction entre les acteurs locaux liés à la musique populaire et l’administration publique dans le cadre du projet public-privé de réaménagement du port de Rio de Janeiro intitulé Porto Maravilha. Le travail de recherche s’est axé sur l’idée que cette interaction serait essentiellement fondée sur la façon dont la “culture” est comprise et utilisée comme ressource capable d’ajouter de la valeur à l’espace urbain, différencier les groupes entre eux et apporter une sustentation au processus d’autonomisation et de légitimation des acteurs. De nouveaux paradigmes urbanistiques, tel celui de “ville créative” (Landry, 2005), proposent d’intégrer la culture locale dans l’élaboration et l’exécution des projets avec la participation d’artistes qui sont perçus comme une source de créativité fondamentale pour rendre la ville plus compétitive dans un monde devenu de plus en plus urbain. Dans cette veine, le projet Porto Maravilha s’inspire franchement des cas de succès de rénovation urbaine créative, stimulant la culture locale et idéalisant le port de Rio comme une “nouvelle carte postale du Brésil”. En partant de la constatation que les acteurs sociaux locaux identifient le potentiel de leurs activités culturelles comme une ressource importante dans ce contexte, nous analysons tout autant les stratégies et les discours élaborés que les ressources dont ils disposent afin d’affirmer leur agentivité. Au-delà de l’action intentionnelle, nous effectuons également des analyses de leurs pratiques culturelles au quotidien en recherchant les éléments qui les constituent. Nous questionnons, par ailleurs, la manière avec laquelle les administrateurs du projet comprennent ces activités musicales et comment ils gèrent les demandes sociales et les contributions créatives de ces groupes.

Operational Flexibility: A Model for Effective Project Management

The aim of this study is to investigate the role of operational flexibility for effective project management in the construction industry. The specific objectives are to: a) Identify the determinants of operational flexibility potential in construction project management b) Investigate the contribution of each of the determinants to operational flexibility potential in the construction industry c) Investigate on the moderating factors of operational flexibility potential in a construction project environment d) Investigate whether moderated operational flexibility potential mediates the path between predictors and effective construction project management e) Develop and test a conceptual model of achieving operational flexibility for effective project management The purpose of this study is to findout ways to utilize flexibility inorder to manage uncertain project environment and ultimately achieve effective project management. In what configuration these operational flexibility determinants are demanded by construction project environment in order to achieve project success. This research was conducted in three phases, namely: (i) exploratory phase (ii) questionnaire development phase; and (iii) data collection and analysis phase. The study needs firm level analysis and therefore real estate developers who are members of CREDAI, Kerala Chapter were considered. This study provides a framework on the functioning of operational flexibility, offering guidance to researchers and practitioners for discovering means to gain operational flexibility in construction firms. The findings provide an empirical understanding on kinds of resources and capabilities a construction firm must accumulate to respond flexibly to the changing project environment offering practitioners insights into practices that build firms operational flexibility potential. Firms are dealing with complex, continuous changing and uncertain environments due trends of globalization, technical changes and innovations and changes in the customers’ needs and expectations. To cope with the increasingly uncertain and quickly changing environment firms strive for flexibility. To achieve the level of flexibility that adds value to the customers, firms should look to flexibility from a day to day operational perspective. Each dimension of operational flexibility is derived from competences and capabilities. In this thesis only the influence on customer satisfaction and learning exploitation of flexibility dimensions which directly add value in the customers eyes are studied to answer the followingresearch questions: “What is the impact of operational flexibility on customer satisfaction?.” What are the predictors of operational flexibility in construction industry? .These questions can only be answered after answering the questions like “Why do firms need operational flexibility?” and “how can firms achieve operational flexibility?” in the context of the construction industry. The need for construction firms to be flexible, via the effective utilization of organizational resources and capabilities for improved responsiveness, is important because of the increasing rate of changes in the business environment within which they operate. Achieving operational flexibility is also important because it has a significant correlation with a project effectiveness and hence a firm’s turnover. It is essential for academics and practitioners to recognize that the attainment of operational flexibility involves different types namely: (i) Modification (ii) new product development and (iii) demand management requires different configurations of predictors (i.e., resources, capabilities and strategies). Construction firms should consider these relationships and implement appropriate management practices for developing and configuring the right kind of resources, capabilities and strategies towards achieving different operational flexibility types.

Thanatos Empresarial : evolución del Sector de la construcción en Colombia.

Esta investigación está orientada hacia la identificación de características de la internacionalización de la economía colombiana, específicamente en el sector de la construcción, los cuales han logrado otorgarle un especial dinamismo durante esta última década. En el desarrollo del documento se evalúan los modelos de internacionalización basados principalmente en tres temas fundamentales; el primero es la teoría económica, el segundo es la teoría como proceso, y por último la teoría de redes. Cada uno de estos modelos basados en su respectiva teoría, enseñan conceptos de cómo podrían las empresas implementar planes para entrar a otros mercados, empezando por países similares tanto en aspectos sociales, económicos, culturales, y políticos, logrando así de esta manera una posición aventajada frente a sus competidores. Al lograr este posicionamiento pueden empezar su expansión a países más lejanos puesto que ya han conocido y fortalecido sus ventajas competitivas, obteniendo una mayor experiencia de adaptación a nuevos mercados, con esto alcanzando captar mayores recursos económicos, de conocimiento y de otras índoles que ayudan a disminuir el riesgo de inversión que realizan las organizaciones en diferentes naciones.

El enfoque del neuromarketing aplicado al mercado colombiano

GLOSARIO • Neuromarketing: El Neuromarketing consiste en la aplicación de las técnicas de investigación de las Neurociencias a la investigación de marketing tradicional. A través de técnicas de medición de la actividad cerebral (como el EGG o la fMRI), las “respuestas” de los entrevistados a distintos estímulos (por ejemplo, anuncios publicitarios) son leídas directamente de su actividad cerebral (Neuromarca) • Neurociencia: La neurociencia estudia la estructura y la función química, farmacología, y patología del sistema nervioso y de cómo los diferentes elementos del sistema nervioso interactúan y dan origen a la conducta (Neurologia y ove) • Mercadeo: Según la American Marketing Asociation (A.M.A.), el marketing es una forma de organizar un conjunto de acciones y procesos a la hora de crear un producto “para crear, comunicar y entregar valor a los clientes, y para manejar las relaciones” y su finalidad es beneficiar a la organización satisfaciendo a los clientes (Revista PYM) • Cerebro: Es la parte más evolucionada y grande del encéfalo. En el cerebro se dan la cognición, el pensamiento y las emociones; también la memoria y el lenguaje. Tiene dos hemisferios, cada uno con 4 lóbulos: frontal, temporal, parietal y occipital. La parte más externa es el cortex cerebral, que tiene unos repliegues que forman circunvoluciones y cisuras (Enciclopedia Salud) • Estrategia Empresarial: Es la que define las diferentes líneas de acción que debe asumir cada uno de los individuos que desempeñan las funciones dentro de la misma y permite a toda organización generar una ventaja competitiva en el mercado en el que desenvuelve sus actividades, generando mayores utilidades y permitiendo aprovechar cada una de las oportunidades dándole un valor agregado (Emagister) • Integración sensorial: Es un proceso Neurológico por el cual las sensaciones que provienen de nuestro entornoy de nuestro cuerpo, son organizadas e interpretadas para su uso (Enciclopedia Salud) • Top of Mind: Es el indicador que revela cuál es la marca que, cuando le preguntan por una categoría específica, se le viene a la mente en primer lugar al mayor porcentaje de personas (Gerente) • Valor Agregado: Valor agregado o valor añadido, en términos de marketing, es una característica o servicio extra que se le da a un producto o servicio, con el fin de darle un mayor valor comercial; generalmente se trata de una característica o servicio poco común, o poco usado por los competidores, y que le da al negocio o empresa cierta diferenciación (Crece Negocios)

Productividad, innovación y uso de tecnologías de información y las comunicaciones (tic) como factores de desarrollo de la micro, pequeña y mediana empresa (mipyme) en Bogotá.

Las TIC han impactado en el funcionamiento de las organizaciones y han aportado a su proceso evolutivo, generando diversos efectos de acuerdo a la función que estas cumplen dentro de la organización. Las TIC como consecuencia se convierten en una estrategia de gestión en un entorno complejo donde permiten alcanzar mejoras en la organización social, la actividad económica, el bienestar y el acceso a la información y el conocimiento. (Cáceres Carrasco & Aceytuno Pérez, 2008)Con el fin de entender los beneficios de las TIC, se deben brindar a los directores herramientas que permitan formular modelos de negocios efectivos de cara a los mercados y enfocadas a la satisfacción de los clientes. Adicionalmente, para las organizaciones el añadir valor, no sólo hace referencia al servicio que están prestando; hay otros factores diferentes al uso de herramientas TIC y la innovación que también son igual de importantes como: los procesos de apoyo, de gestión que se encuentran de fondo y que hacen posible brindar un servicio al mercado, en estos procesos se encuentran aplicaciones de procedimientos amigables y fáciles de articular, temas como la responsabilidad empresarial, relación y comunicación con competidores dentro del mismo sector, es justamente en las relaciones con los clientes, que las TIC y el uso de Internet puede tener incidencia en los modelos de negocios a través de actividades como el comercio electrónico, el mercadeo electrónico, el mercadeo en línea entre otros. Existen investigaciones acerca de estos temas: innovación, TI, pero no se han establecido relaciones entre ellos, debido a su novedad. Diferentes experiencias laborales de los investigadores en el uso de las TIC como herramienta en la organización de información permiten que surja la idea de llevar a cabo este proyecto abarcando la realidad bogotana de las MiPyme. La presente investigación con un enfoque cualitativo hace una revisión bibliográfica, y bajo la mirada teórica se analiza la relación que tienen los factores de desarrollo que se evidenciaron como son la innovación y el uso de herramientas TIC, como variables dependientes de la productividad de las MiPyme en Bogotá, Colombia, involucrando temas que se relacionan con distintos campos como la tecnología, políticas gubernamentales, y economía.

The extrapolation problem and how population modeling can help

We argue that population modeling can add value to ecological risk assessment by reducing uncertainty when extrapolating from ecotoxicological observations to relevant ecological effects. We review other methods of extrapolation, ranging from application factors to species sensitivity distributions to suborganismal (biomarker and "-omics'') responses to quantitative structure activity relationships and model ecosystems, drawing attention to the limitations of each. We suggest a simple classification of population models and critically examine each model in an extrapolation context. We conclude that population models have the potential for adding value to ecological risk assessment by incorporating better understanding of the links between individual responses and population size and structure and by incorporating greater levels of ecological complexity. A number of issues, however, need to be addressed before such models are likely to become more widely used. In a science context, these involve challenges in parameterization, questions about appropriate levels of complexity, issues concerning how specific or general the models need to be, and the extent to which interactions through competition and trophic relationships can be easily incorporated.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.