-
We use an autoethnographic case study of a Latinx high school student from an agricultural community in California to highlight how AI is learned outside classrooms and how her personal background influenced her social-justice oriented applications of AI techn…
arxiv
Stephanie Tena-Meza, Miroslav Suzara, AJ Alvero
2021-08-30T16:36:52Z
置信度 0.78
cs.CY
-
The rapid adoption of generative artificial intelligence (GenAI) in schools raises concerns about students' uncritical reliance on its outputs. Effective use of large language models (LLMs) requires not only technical knowledge but also the ability to monitor,…
arxiv
O. Clerc, R. Abdelghani, C. Desvaux, E. Poisson 等
2026-04-02T12:19:43Z
置信度 0.78
cs.CY
-
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable computational and data s…
arxiv
The Genomic Data Science Community Network, Rosa Alcazar, Maria Alvarez, Rachel Arnold 等
2022-01-20T20:36:18Z
置信度 0.78
q-bio.OTcs.CY
-
We present preliminary results on the XMM-Newton Survey Science Centre medium sensitivity survey (XMS), with 0.5-4.5 keV flux limit 2 10^{-14} erg/cm2/s. At present, 19 fields have been examined with a total of 239 X-ray sources. Identifications for about 2/3 …
arxiv
X. Barcons, F. J. Carrera, M. T. Ceballos, S. Mateos 等
2002-11-25T12:21:45Z
置信度 0.78
astro-ph
-
Very soon, millions of AI agents will proliferate across the economy, autonomously taking billions of actions. Inevitably, things will go wrong. Humans will be defrauded, injured, even killed. Law will somehow have to govern the coming wave. But when an AI cau…
arxiv
Yonathan Arbel, Peter Salib, Simon Goldstein
2026-02-24T23:04:17Z
置信度 0.78
cs.CYcs.AI
-
There is no 'ordinary' when it comes to AI. The human-AI experience is extraordinarily complex and specific to each person, yet dominant measures such as usability scales and engagement metrics flatten away nuance. We argue for AI phenomenology: a research sta…
arxiv
Bhada Yun, Evgenia Taranova, Dana Feng, Renn Su 等
2026-03-09T23:26:46Z
置信度 0.78
cs.HCcs.AI
-
As multi-agent AI systems become increasingly autonomous, evidence shows they can develop collusive strategies similar to those long observed in human markets and institutions. While human domains have accumulated centuries of anti-collusion mechanisms, it rem…
arxiv
Jamiu Idowu, Ahmed Almasoud, Ayman Alfahid
2026-01-01T14:30:37Z
置信度 0.78
cs.MAcs.AIcs.CY
-
GeoAI, or geospatial artificial intelligence, is an exciting new area that leverages artificial intelligence (AI), geospatial big data, and massive computing power to solve problems with high automation and intelligence. This paper reviews the progress of AI i…
arxiv
Wenwen Li
2023-12-19T20:23:18Z
置信度 0.78
cs.CYcs.AI
-
This paper explores the transformative role of artificial intelligence (AI) in enhancing scientific research, particularly in the fields of brain science and social sciences. We analyze the fundamental aspects of human research and argue that it is high time f…
arxiv
Feng Xiong, Xinguo Yu, Hon Wai Leong
2024-11-16T11:13:23Z
置信度 0.78
cs.HCcs.AI
-
Large language models (LLMs) have exhibited exceptional capabilities in natural language understanding and generation, image recognition, and multimodal tasks, charting a course towards AGI and emerging as a central issue in the global technological race. This…
arxiv
Guoqiang Liang, Jingqian Gong, Mengxuan Li, Gege Lin 等
2025-11-19T11:57:22Z
置信度 0.78
cs.CLcs.AI
-
AI models are rapidly becoming embedded in all aspects of nuclear energy research and work but the safety, security, and safeguards consequences of this embedding are not well understood. In this paper, we call for the creation of an anticipatory system of gov…
arxiv
Aditi Verma, Elizabeth Williams
2025-04-16T03:43:15Z
置信度 0.78
cs.CYcs.AIphysics.soc-ph
-
Data science and technology offer transformative tools and methods to science. This review article highlights latest development and progress in the interdisciplinary field of data-driven plasma science (DDPS). A large amount of data and machine learning algor…
arxiv
Rushil Anirudh, Rick Archibald, M. Salman Asif, Markus M. Becker 等
2022-05-31T14:37:06Z
置信度 0.78
physics.plasm-ph
-
This position paper discusses the benefits of longitudinal behavioural research with customised AI tools for exploring the opportunities and risks of synthetic relationships. Synthetic relationships are defined as "continuing associations between humans and AI…
arxiv
Alfio Ventura, Nils Köbis
2024-12-12T09:13:43Z
置信度 0.78
cs.HCcs.AIcs.CY
-
The study of transient and variable low-frequency radio sources is a key goal for LOFAR, with an extremely broad science case ranging from relativistic jets sources to pulsars, exoplanets, radio bursts at cosmological distances, the identification of gravitati…
arxiv
Rob Fender, Ralph Wijers, Ben Stappers, the LOFAR Transients Key Science Project
2008-05-28T13:36:24Z
置信度 0.78
astro-ph
-
This paper examines how competing sociotechnical imaginaries of artificial intelligence (AI) risk shape governance decisions and regulatory constraints. Drawing on concepts from science and technology studies, we analyse three dominant narrative groups: existe…
arxiv
Ninell Oldenburg, Gleb Papyshev
2025-08-15T09:57:56Z
置信度 0.78
cs.CYcs.AI
-
Advanced analytics science methods have enabled combining the power of artificial and human intelligence, creating \textit{centaurs} that allow superior decision-making. Centaurs are hybrid human-algorithm models that combine both formal analytics and human in…
arxiv
Soroush Saghafian, Lihi Idan
2024-06-16T13:44:41Z
置信度 0.78
cs.AIcs.LG
-
This Journal of Informetrics special issue aims to improve our understanding of the structure and dynamics of science by reviewing and advancing existing conceptualizations and models of scholarly activity. Several of these conceptualizations and models have v…
arxiv
Katy Boerner, Andrea Scharnhorst
2009-03-20T16:35:18Z
置信度 0.78
cs.DLphysics.soc-ph
-
crossref
2022-11-15T17:03:19Z
置信度 0.70
-
crossref
2022-11-15T17:03:19Z
置信度 0.70
-
Generative AI has brought innovations across multiple fields, offering great tools for enhanced communication and efficiency. This project focused on developing a custom AI chatbot using OpenAI's Chat GPT (GPT-4o) to support the Fermilab communications team. A…
crossref
Diego Valle
2024-08-15T02:28:58Z
置信度 0.70
-
Abstract Subject area classification is an important first phase in the entire process involved in bibliometrics. In this paper, we explore the possibility of using automated algorithms for classifying scientific papers related to Artificial Intelligence at th…
crossref
Evi Sachini, Konstantinos Sioumalas-Christodoulou, Stefanos Christopoulos, Nikolaos Karampekios
2022-11-15T15:10:19Z
置信度 0.70
-
This section focuses on applying critical thinking to AI-generated content. It presents techniques for identifying errors, verifying information, and analyzing outputs for bias, relevance, and accuracy. Strategies for evaluating text and images are discussed a…
crossref
Anand Rao, Stefan Bauschard
2026-08-04T16:43:27Z
置信度 0.70
-
Investigating CO adsorption on Cu(111) and Rh(111) surfaces using machine learning exchange-correlation functionals Xinyuan
crossref
Weihua Wang, Gian-Marco Rignanese
2025-04-25T22:48:51Z
置信度 0.70
-
This part explains the nature of generative AI and its distinction from traditional AI systems. It describes how these tools create new content by identifying patterns and generating text, images, or other outputs. The section introduces common AI tools, their…
crossref
Anand Rao, Stefan Bauschard
2026-08-04T16:43:27Z
置信度 0.70
-
This part examines how academic integrity principles apply to the use of generative AI in coursework. It emphasizes appropriate decision-making, accurate documentation, and awareness of institutional AI policies. Guidance is provided on distinguishing between …
crossref
Anand Rao, Stefan Bauschard
2026-08-04T16:43:27Z
置信度 0.70
-
This part explores the key advantages and limitations of generative AI. It outlines methods for critical evaluation of AI-generated content, highlights issues such as bias, and considers environmental impacts. The section addresses risks including misinformati…
crossref
Anand Rao, Stefan Bauschard
2026-08-04T16:43:27Z
置信度 0.70
-
The final part introduces the principles of prompt engineering for generative AI. It explains how to construct effective prompts, refine them through iteration, and apply techniques ethically in academic contexts. Key elements that improve response quality are…
crossref
Anand Rao, Stefan Bauschard
2026-08-04T16:43:33Z
置信度 0.70
-
crossref
Shuo Wang
2025-10-15T11:36:30Z
置信度 0.70
-
crossref
Evi Sachini, Konstantinos Sioumalas-Christodoulou, Stefanos Christopoulos, Nikolaos Karampekios
2022-11-15T17:03:19Z
置信度 0.70
-
crossref
2026-07-15T06:46:11Z
置信度 0.70
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
Annika Jacobsen, Erik van Dijk, Halima Mouhib, Bas Stringer 等
2023-07-05T10:12:55Z
置信度 0.78
q-bio.BM
-
Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations. Results: We present a quan…
arxiv
Biraja Ghoshal
2026-01-02T11:33:09Z
置信度 0.78
q-bio.QMcs.ET
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
K. Anton Feenstra, Sanne Abeln
2018-01-29T10:54:27Z
置信度 0.78
q-bio.BM
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
Juami H. M. van Gils, Maurits Dijkstra, Halima Mouhib, Arriën Symon Rauh 等
2023-07-05T10:13:15Z
置信度 0.78
q-bio.BM
-
We study the combined influence of amino acid composition and chain length on the thermal stability of protein structures. A new parameterization of the internal free energy is considered, as the sum of hydrophobic effect, hydrogen-bond and de-hydration energy…
arxiv
Antonio Deiana, Kana Shimizu, Andrea Giansanti
2010-12-29T11:50:28Z
置信度 0.78
q-bio.GN
-
Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer percept…
arxiv
Zeming Lin, Jack Lanchantin, Yanjun Qi
2016-05-10T13:31:52Z
置信度 0.78
cs.LG
-
This paper focuses on three critical problems on protein classification. Firstly, Carbohydrate-active enzyme (CAZyme) classification can help people to understand the properties of enzymes. However, one CAZyme may belong to several classes. This leads to Multi…
arxiv
Zhuangwei Shi, Bo Li
2022-04-20T14:34:29Z
置信度 0.78
q-bio.BMcs.LG
-
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state…
arxiv
Tatjana Škrbić, Amos Maritan, Achille Giacometti, Jayanth R. Banavar
2021-01-27T22:26:16Z
置信度 0.78
q-bio.BMcond-mat.softcond-mat.stat-mechphysics.bio-ph
-
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common approach to diversity is…
arxiv
T. Garel
2003-05-03T06:00:39Z
置信度 0.78
cond-mat.softcond-mat.dis-nncond-mat.stat-mechq-bio.BM
-
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum chemistry, biology o…
arxiv
Vasundhara Gadiyaram, Smitha Vishveshwara, Saraswathi Vishveshwara
2019-12-25T06:52:05Z
置信度 0.78
q-bio.MNcond-mat.stat-mech
-
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global networ…
arxiv
Peter Csermely, Kuljeet Singh Sandhu, Eszter Hazai, Zsolt Hoksza 等
2011-01-31T07:55:53Z
置信度 0.78
q-bio.MNcond-mat.dis-nnphysics.bio-ph
-
Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient nature. Here we describ…
arxiv
Timothy D. Cummins, Gopal P. Sapkota
2016-06-14T08:34:04Z
置信度 0.78
q-bio.MNq-bio.BM
-
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological e…
arxiv
Zhuoyi Liu, Alex T. Grigas, Jacob Sumner, Edward Knab 等
2024-05-13T17:55:52Z
置信度 0.78
physics.bio-phq-bio.BM
-
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a…
arxiv
Alex T. Grigas, Zhe Mei, John D. Treado, Zachary A. Levine 等
2020-01-05T03:32:15Z
置信度 0.78
q-bio.BMcond-mat.soft
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
Juami H. M. van Gils, Erik van Dijk, Ali May, Halima Mouhib 等
2023-07-05T10:13:08Z
置信度 0.78
q-bio.BM
-
Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere with those or to guide…
arxiv
Xiaotong Xu, Alexandre M. J. J. Bonvin
2024-07-23T10:51:35Z
置信度 0.78
q-bio.BMcs.AI
-
Most of the problems in bioinformatics are now the challenges in computing. This paper aims at building a classifier based on Multiple Attractor Cellular Automata (MACA) which uses fuzzy logic. It is strengthened with an artificial Immune System Technique (AIS…
arxiv
Pokkuluri Kiran Sree, Inampudi Ramesh Babu
2014-03-24T12:37:11Z
置信度 0.78
cs.CEcs.LG
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
Juami H. M. van Gils, Halima Mouhib, Erik van Dijk, Maurits Dijkstra 等
2023-07-05T10:13:10Z
置信度 0.78
q-bio.BM
-
A structure prediction method is presented based on the Minima Hopping method. Optimized moves on the configurational enthalpy surface are performed to escape local minima using variable cell shape molecular dynamics by aligning the initial atomic and cell vel…
arxiv
Maximilian Amsler, Stefan Goedecker
2010-07-12T22:44:19Z
置信度 0.78
cond-mat.mtrl-sciphysics.comp-ph
-
We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic conf…
arxiv
A. Brenda Guzovsky, Nicholas P. Schafer, Peter G. Wolynes, Diego U. Ferreiro
2018-12-14T14:47:03Z
置信度 0.78
q-bio.BM
-
In Dec 2020, the results of AlphaFold2 were presented at CASP14, sparking a revolution in the field of protein structure predictions. For the first time, a purely computational method could challenge experimental accuracy for structure prediction of single pro…
arxiv
Arne Elofsson
2022-12-15T10:25:44Z
置信度 0.78
q-bio.BM
-
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and …
arxiv
Yufei Huang, Siyuan Li, Jin Su, Lirong Wu 等
2023-10-14T08:43:42Z
置信度 0.78
cs.LGcs.AIq-bio.QM
-
Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the constituents of all proteins.…
arxiv
Mahmood A. Rashid, Firas Khatib, Abdul Sattar
2015-10-09T19:17:12Z
置信度 0.78
cs.CEq-bio.BM
-
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the biochemical mechanisms…
arxiv
K. K Senapati, G. Sahoo, D. Bhaumik
2010-06-14T19:38:28Z
置信度 0.78
cs.CEq-bio.BM
-
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview o…
arxiv
Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2017-12-01T17:09:40Z
置信度 0.78
q-bio.BM
-
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for protein structure predicti…
arxiv
Manuel Bezerra-Brandao, Ronaldo Romario Tunque Cahui, Layla Hirsh
2024-07-10T16:41:19Z
置信度 0.78
cs.SEcs.DB
-
Biological AI models increasingly predict complex cellular responses, yet their learned representations remain disconnected from the molecular processes they aim to capture. We present CDT-III, which extends mechanism-oriented AI across the full central dogma:…
arxiv
Nobuyuki Ota
2026-03-24T15:57:23Z
置信度 0.78
cs.LGq-bio.GN
-
Outcome prediction is crucial for head and neck cancer patients as it can provide prognostic information for early treatment planning. Radiomics methods have been widely used for outcome prediction from medical images. However, these methods are limited by the…
arxiv
Mingyuan Meng, Lei Bi, Dagan Feng, Jinman Kim
2022-11-10T08:28:56Z
置信度 0.78
eess.IVcs.CVcs.LG
-
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and folding of the secondary …
arxiv
Yanlin Zhou, Kai Tan, Xinyu Shen, Zheng He 等
2024-02-29T12:24:20Z
置信度 0.78
q-bio.BMcs.LG
-
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to develop supplementa…
arxiv
Jianzhu Ma
2015-10-19T20:46:04Z
置信度 0.78
cs.CEcs.LGq-bio.BM
-
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and universality of ligand bind…
arxiv
Akira R. Kinjo, Haruki Nakamura
2008-10-08T00:29:42Z
置信度 0.78
q-bio.BM
-
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein structure prediction,…
arxiv
Michael C. Prentiss, Corey Hardin, Michael P. Eastwood, Chenghong Zong 等
2006-06-12T13:37:23Z
置信度 0.78
q-bio.BM
-
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use of lattice models to …
arxiv
D. Thirumalai, D. K. Klimov
2001-01-04T20:33:29Z
置信度 0.78
cond-mat.softq-bio
-
To explain experimentally observed oscillatory dynamics of highly efficient process of excitation energy transfer (EET) in Fenna-Matthews-Olson (FMO) complex, most theoretical models assume the same local protein environment around all the bacteriochlorophyll-…
arxiv
Davinder Singh, Shubhrangshu Dasgupta
2016-04-29T06:29:00Z
置信度 0.78
physics.bio-phphysics.chem-phquant-ph
-
Models such as AlphaFold2 and OpenFold have transformed protein structure prediction, yet their inner workings remain poorly understood. We present a methodology to systematically evaluate the contribution of individual OpenFold components to structure predict…
arxiv
Tyler L. Hayes, Giri P. Krishnan
2025-11-06T20:41:34Z
置信度 0.78
q-bio.BMcs.AI
-
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships between protein structu…
arxiv
Daniel Bonetti, Alexandre Delbem, Dorival Leão, Jochen Einbeck
2019-01-04T11:26:42Z
置信度 0.78
q-bio.BM
-
Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select' protein conformation…
arxiv
Thomas R. Weikl, Fabian Paul
2014-09-09T03:36:46Z
置信度 0.78
q-bio.BM
-
Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter complex ambient conditio…
arxiv
Zechuan Yu, Denvid Lau
2016-07-13T03:32:46Z
置信度 0.78
cond-mat.mtrl-sciphysics.bio-phq-bio.BM
-
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query proteins and constru…
arxiv
Jian Peng
2013-06-19T04:42:34Z
置信度 0.78
q-bio.BM
-
Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restrict…
arxiv
Sirui Liu, Jun Zhang, Haotian Chu, Min Wang 等
2022-06-24T14:08:44Z
置信度 0.78
q-bio.BMcs.LG
-
The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial proteomics data remains sca…
arxiv
Zhaorui Jiang, Yingfang Yuan, Lei Hu, Wei Pang
2026-02-05T16:04:03Z
置信度 0.78
cs.AI
-
Native contacts between residues could be predicted from the amino acid sequence of proteins, and the predicted contact information could assist the de novo protein structure prediction. Here, we present a novel pipeline of a residue contact predictor AmoebaCo…
arxiv
Wenzhi Mao, Wenze Ding, Haipeng Gong
2019-05-28T06:54:24Z
置信度 0.78
q-bio.BM
-
While monomer protein structure prediction tools boast impressive accuracy, the prediction of protein complex structures remains a daunting challenge in the field. This challenge is particularly pronounced in scenarios involving complexes with protein chains f…
arxiv
Xiaomin Fang, Jie Gao, Jing Hu, Lihang Liu 等
2024-04-16T03:29:37Z
置信度 0.78
q-bio.BMcs.AI
-
Predicting the biophysical and functional properties of proteins is essential for in silico protein design. Machine learning has emerged as a promising technique for such prediction tasks. However, the relative scarcity of in vitro annotations means that these…
arxiv
Jacob Beck, Shikha Surana, Manus McAuliffe, Oliver Bent 等
2024-10-10T20:19:35Z
置信度 0.78
cs.LG
-
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free energy barrier. We …
arxiv
C. Clementi, S. S. Plotkin
2004-07-15T01:44:42Z
置信度 0.78
q-bio.BM
-
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is tightly connected to…
arxiv
Leila Khalatbari, Mohammad Reza Kangavari, Saeid Hosseini, Hongzhi Yin 等
2018-06-17T15:18:31Z
置信度 0.78
cs.CE
-
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding models such as ESM3, …
arxiv
Colby T. Ford, Samee Ullah, Dinler Amaral Antunes, Tarsis Gesteira Ferreira
2025-02-01T17:58:45Z
置信度 0.78
q-bio.BM
-
In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with high accuracy and con…
arxiv
Devlina Chakravarty, Myeongsang Lee, Lauren L. Porter
2024-10-18T22:52:17Z
置信度 0.78
q-bio.BM
-
The ability to make zero-shot predictions about the fitness consequences of protein sequence changes with pre-trained machine learning models enables many practical applications. Such models can be applied for downstream tasks like genetic variant interpretati…
arxiv
Arnav Sharma, Anthony Gitter
2025-04-23T17:01:09Z
置信度 0.78
q-bio.QMcs.LGq-bio.BM
-
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range contacts could help topolo…
arxiv
Siqi Sun
2020-08-31T22:37:16Z
置信度 0.78
q-bio.QMcs.LGstat.ML
-
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction (including our own FARNA-F…
arxiv
Kyle Beauchamp, Parin Sripakdeevong, Rhiju Das
2011-03-15T20:40:15Z
置信度 0.78
q-bio.BMphysics.bio-phphysics.chem-ph
-
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms to protein sequence …
arxiv
Manzi Kevin Maxime
2025-12-09T13:58:47Z
置信度 0.78
cs.AI
-
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introducti…
arxiv
Maurits Dijkstra, Punto Bawono, Isabel Houtkamp, Jose Gavaldá-Garciá 等
2023-07-05T10:13:02Z
置信度 0.78
q-bio.BM
-
Protein language models have revolutionized structure prediction, but their nonlinear nature obscures how sequence representations inform structure prediction. While sparse autoencoders (SAEs) offer a path to interpretability here by learning linear representa…
arxiv
Nithin Parsan, David J. Yang, John J. Yang
2025-03-11T17:57:29Z
置信度 0.78
q-bio.BMcs.AIcs.LG
-
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge. The traditional met…
arxiv
Musa Azeem, Homayoun Valafar
2024-07-09T16:54:36Z
置信度 0.78
q-bio.BMcs.CE
-
Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotat…
arxiv
Taewon Kim, Hyosoon Jang, Hyunjin Seo, Seonghwan Seo 等
2026-05-21T08:07:36Z
置信度 0.78
q-bio.BMcs.AI
-
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins. In this letter we r…
arxiv
Dmitry Melnikov, Alyson B. F. Neves
2019-08-30T13:48:18Z
置信度 0.78
q-bio.BMcond-mat.softhep-phhep-thphysics.bio-ph
-
Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure refinement protocols. A trem…
arxiv
Surbhi Dhingra, Ramanathan Sowdhamini, Frédéric Cadet, Bernard Offmann
2020-02-16T16:36:58Z
置信度 0.78
q-bio.QMq-bio.BM
-
The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in amino acid networks b…
arxiv
Miklos A. Antal, Csaba Bode, Peter Csermely
2008-02-16T13:55:00Z
置信度 0.78
q-bio.MNnlin.AOphysics.bio-phq-bio.BM
-
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter presents a step-by-step …
arxiv
Victor Reys, Marco Giulini, Alexandre M. J. J. Bonvin
2026-03-18T01:11:36Z
置信度 0.78
q-bio.BM
-
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates pred…
arxiv
Iddo Drori, Darshan Thaker, Arjun Srivatsa, Daniel Jeong 等
2019-11-09T00:21:17Z
置信度 0.78
q-bio.BMcs.LGstat.ML
-
AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from the homologous seque…
arxiv
Xiaomin Fang, Fan Wang, Lihang Liu, Jingzhou He 等
2022-07-28T07:30:33Z
置信度 0.78
q-bio.BMcs.AIcs.LGq-bio.QM
-
Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and structure informati…
arxiv
Runze Ma, Chengxin He, Huiru Zheng, Xinye Wang 等
2024-11-18T08:23:26Z
置信度 0.78
q-bio.BM
-
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local fluctuations, the dynamics …
arxiv
J. Copperman, M. G. Guenza
2015-09-29T00:47:09Z
置信度 0.78
physics.bio-phcond-mat.softq-bio.BM
-
We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with subsecond prediction t…
arxiv
Evan Weissburg, Ian Bulovic
2018-09-24T20:36:58Z
置信度 0.78
q-bio.QMq-bio.BM
-
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solv…
arxiv
Zhe Mei, John D. Treado, Alex T. Grigas, Zachary A. Levine 等
2019-07-18T18:27:42Z
置信度 0.78
q-bio.BMphysics.bio-ph
-
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000 - 16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in pro…
arxiv
Jingyi Jessica Li, Peter J. Bickel, Mark D. Biggin
2012-12-03T23:33:19Z
置信度 0.78
q-bio.GN
-
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availabi…
arxiv
Kaihui Cheng, Ce Liu, Qingkun Su, Jun Wang 等
2024-08-22T14:12:50Z
置信度 0.78
cs.LGcs.AI
-
Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus o…
arxiv
Wei-Mou Zheng
2003-07-16T02:34:30Z
置信度 0.78
physics.bio-phphysics.data-anq-bio.BM
-
The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is sig…
arxiv
Le Zhang, Jiayang Chen, Tao Shen, Yu Li 等
2023-06-02T14:13:50Z
置信度 0.78
q-bio.QMcs.CEcs.LGq-bio.BM