pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1186/s13071-020-04342-5

Anopheles metabolic proteins in malaria transmission, prevention and control: a review
Cited by: 15
Author(s): Eunice Adedeji, Olubanke Olujoke Ogunlana, Segun Fatumo, Thomas Beder, Yvonne Ukamaka Ajamma, Rainer Koenig, Ezekiel Adebiyi
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13071-020-04019-z

Insights about the structure of farnesyl diphosphate synthase (FPPS) and the activity of bisphosphonates on the proliferation and ultrastructure of Leishmania and Giardia
Cited by: 11
Author(s): Ana Paula Rocha Gadelha, Claudia Maia Brigagao, Martha Barros da Silva, Aline Beatriz Mello Rodrigues, Ana Carolina Ramos Guimarães, Fernando Paiva, Wanderley de Souza, Cristina Henriques
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-018-2703-1

A novel progesterone receptor membrane component (PGRMC) in the human and swine parasite Taenia solium: implications to the host-parasite relationship
Cited by: 10
Author(s): Hugo Aguilar-Díaz, Karen Elizabeth Nava-Castro, Galileo Escobedo, Lenin Domínguez-Ramírez, Martìn García-Varela, Víctor Hugo Del Río-Araiza, Margarita Isabel Palacios-Arreola, Jorge Morales‐Montor
Software Mentions: 1
Published: over 8 years ago

10.1186/s13071-015-1006-z

ANISERP: a new serpin from the parasite Anisakis simplex
Cited by: 9
Author(s): Elizabeth Valdivieso, María Jesús Perteguer, Carolina Hurtado, Pamela Campioli, Esperanza Rodríguez, Ana Saborido, Victoria Martínez-Sernández, Paulino Gómez‐Puertas, Florencio M. Ubeira, Teresa Gárate
Software Mentions: 1
Published: about 11 years ago

10.1186/s13071-016-1391-y

Unique PFK regulatory property from some mosquito vectors of disease, and from Drosophila melanogaster
Cited by: 11
Author(s): Rodrigo Dutra Nunes, Nelilma C. Romeiro, Hugo Tremonte de Carvalho, Jean Ribeiro Moreira, Mauro Sola‐Penna, Mário A.C. Silva-Neto, Glória R.C. Braz
Software Mentions: 1
Published: over 10 years ago

10.1186/s13071-019-3833-9

Vaccination of mice with a recombinant novel cathepsin B inhibits Trichinella spiralis development, reduces the fecundity and worm burden
Cited by: 32
Author(s): Jing Cui, Yang Han, Xin Yue, Fang Liu, Yan Song, Shu Wei Yan, Jun Lei, Xi Zhang, Peng Jiang, Zhong Quan Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-020-3981-y

Molecular characterization of a Trichinella spiralis elastase-1 and its potential as a diagnostic antigen for trichinellosis
Cited by: 34
Author(s): Hu Chen, Peng Jiang, Xin Yue, Jie Zeng, Xin Zhuo Zhang, Yan Song, Ruo Dan Liu, Xi Zhang, Zhong Quan Wang, Jing Cui
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-018-2667-1

Characterization and expression analysis of a newly identified glutathione S-transferase of the hard tick Haemaphysalis longicornis during blood-feeding
Cited by: 28
Author(s): Emmanuel Pacia Hernandez, Kodai Kusakisako, Melbourne Rio Talactac, Remil Linggatong Galay, Takeshi Hatta, Tomohide Matsuo, Kozo Fujisaki, Naotoshi Tsuji, Tetsuya Tanaka
Software Mentions: 1
Published: over 8 years ago

10.1186/s13071-019-3767-2

Identification of linear epitopes in SjSP-13 of Schistosoma japonicum using a GST-peptide fusion protein microplate array
Cited by: 3
Author(s): Li Ma, Wenrong Zhao, Xin Hou, Mengmeng Liu, Yanna Li, Li Shen, Xindong Xu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13071-015-1070-4

Mosquito Rasputin interacts with chikungunya virus nsP3 and determines the infection rate in Aedes albopictus
Cited by: 38
Author(s): Jelke J. Fros, Corinne Geertsema, Karima Zouache, Jim Baggen, Natalia E. Domeradzka, Daniël M van Leeuwen, Jacky Flipse, Just M. Vlak, Anna‐Bella Failloux, Gorben P. Pijlman
Software Mentions: 1
Published: almost 11 years ago

10.1186/1756-3305-6-156

TIMPs of parasitic helminths – a large-scale analysis of high-throughput sequence datasets
Cited by: 19
Author(s): Cinzia Cantacessi, Andreas Hofmann, Darren Pickering, Séverine Navarro, Makedonka Mitreva, Alex Loukas
Software Mentions: 1
Published: about 13 years ago

10.1186/s13071-020-04495-3

Downregulated RPS-30 in Angiostrongylus cantonensis L5 plays a defensive role against damage due to oxidative stress
Cited by: 3
Author(s): Weiwei Sun, Xiumei Yan, Qing Shi, Yuan-Jiao Zhang, Junting Huang, Huicong Huang, Hengzhen Shi, Bowen Yan
Software Mentions: 1
Published: over 5 years ago

10.1186/s13071-021-04933-w

The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions
Cited by: 10
Author(s): Chloé Suzanne Berger, Jérôme Laroche, Halim Maaroufi, Hélène Martin, Kyung‐Mee Moon, Christian R. Landry, Leonard J. Foster, Nadia Aubin‐Horth
Software Mentions: 1
Published: almost 5 years ago

10.1155/2019/9024894

Novel Compound Heterozygous PRKN Variants in a Han-Chinese Family with Early-Onset Parkinson’s Disease
Cited by: 2
Author(s): Kuan Fan, Pengzhi Hu, Chengyuan Song, Xiong Deng, Jie Wen, Yiming Liu, Hao Deng
Software Mentions: 1
Published: over 6 years ago

10.3390/pathogens10070861

Rapid Generation of Coronaviral Immunity Using Recombinant Peptide Modified Nanodiamonds
Cited by: 9
Author(s): Rostyslav Bilyy, Quentin Pagneux, Nathan François, Galyna Bila, Roman Grytsko, Yuri Lebedin, Alexandre Barras, Jean Dubuisson, Sandrine Belouzard, Karin Séron, Rabah Boukherroub, Sabine Szunerits
Software Mentions: 1
Published: about 5 years ago

10.3390/pathogens10040438

Longitudinal Development of Antibody Responses in COVID-19 Patients of Different Severity with ELISA, Peptide, and Glycan Arrays: An Immunological Case Series
Cited by: 18
Author(s): Jasmin Heidepriem, Christine Dahlke, Robin Kobbe, René Santer, Till Koch, Anahita Fathi, Bruna Mara Silva Seco, My L. Ly, Stefan Schmiedel, Dorothee Schwinge, Sonia Serna, Katrin Sellrie, Niels‐Christian Reichardt, Peter H. Seeberger, Marylyn M. Addo, Felix F. Loeffler
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10040437

Association of Bovine Leukemia Virus-Induced Lymphoma with BoLA-DRB3 Polymorphisms at DNA, Amino Acid, and Binding Pocket Property Levels
Cited by: 18
Author(s): Chieh-Wen Lo, Shin‐nosuke Takeshima, Kōsuke Okada, Etsuko Saitou, Tatsuo Fujita, Yasunobu Matsumoto, Satoshi Wada, Hidetoshi Inoko, Yoko Aida
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10091199

Canine Morbillivirus from Colombian Lineage Exhibits In Silico and In Vitro Potential to Infect Human Cells
Cited by: 5
Author(s): Santiago Rendón-Marín, Carolina Quintero-Gil, Diego Guerra, Carlos Muskus, Julián Ruíz-Sáenz
Software Mentions: 1
Published: almost 5 years ago

10.3390/pathogens9100829

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?
Cited by: 45
Author(s): Tarek Alouane, Meriem Laamarti, Abdelomunim Essabbar, Mohammed Hakmi, El Mehdi Bouricha, Mohammed Walid Chemao-Elfihri, Souad Kartti, Nasma Boumajdi, Houda Bendani, Rokia Laamarti, Fatima Ghrifi, Loubna Allam, Tarik Aanniz, Mouna Ouadghiri, Naïma El Hafidi, Rachid El Jaoudi, Houda Benrahma, Jalil El Attar, Rachid Mentag, Laïla Sbabou, Chakib Nejjari, Saaïd Amzazi, Lahcen Belyamani, Azeddine Ibrahimi
Software Mentions: 1
Published: almost 6 years ago

10.3390/pathogens10070902

Cyclophilins and Their Roles in Hepatitis C Virus and Flavivirus Infections: Perspectives for Novel Antiviral Approaches
Cited by: 4
Author(s): Carla E. Gallardo-Flores, Che C. Colpitts
Software Mentions: 1
Published: about 5 years ago

10.1186/s12969-021-00612-3

Comment on: homozygous variant p. Arg90His in NCF1 is associated with early-onset interferonopathy: a case report
Cited by: 1
Author(s): George N. Goulielmos, Maria I. Zervou, Elias Eliopoulos
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.1674

Initiating a watch list for Ebola virus antibody escape mutations
Cited by: 35
Author(s): Craig R. Miller, Erin L. Johnson, Aran Z. Burke, Kyle Martin, Tanya A. Miura, Holly A. Wichman, Celeste J. Brown, F. Marty Ytreberg
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.4270

Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies
Cited by: 11
Author(s): Yasemin Budama‐Kilinc, Rabia Çakır-Koç, Serda Kecel‐Gunduz, Yağmur Kökcü, Bilge Bıçak, Hande Mutlu, Ayşen E. Özel
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.2289

A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungusOrpinomycessp. strain C1A
Cited by: 24
Author(s): J. Morrison, Mostafa S. Elshahed, Noha H. Youssef
Software Mentions: 1
Published: about 10 years ago

10.7717/peerj.5780

Plant-derived chimeric antibodies inhibit the invasion of human fibroblasts byToxoplasma gondii
Cited by: 7
Author(s): Sherene Swee Yin Lim, Kek Heng Chua, Greta Nölke, Holger Spiegel, Wai Leong Goh, Sek C. Chow, Boon Pin Kee, Rainer Fischer, Stefan Schillberg, Rofina Yasmin Othman
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.85

Molecular modeling and pharmacophore elucidation study of the Classical Swine Fever virus helicase as a promising pharmacological target
Cited by: 22
Author(s): Dimitriοs Vlachakis, Σοφία Κοσσίδα
Software Mentions: 1
Published: about 13 years ago

10.7717/peerj.1528

Activity and biophysical inhibition resistance of a novel synthetic lung surfactant containing Super-Mini-B DATK peptide
Cited by: 8
Author(s): Robert H. Notter, Zhengdong Wang, Frans J. Walther
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.3160

In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease
Cited by: 15
Author(s): Manoj Kumar, Subhash Chandra Parija
Software Mentions: 1
Published: about 9 years ago

10.7717/peerj.11232

Bioinformatic prediction of immunodominant regions in spike protein for early diagnosis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Cited by: 5
Author(s): Shihao Zhuang, Lingli Tang, Yufeng Dai, Xiaojing Feng, Yutao Fang, Haoneng Tang, Ping Jiang, Xiang Wu, Hezhi Fang, Hongzhi Chen
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.10143

In silico structural homology modeling and characterization of multiple N-terminal domains of selected bacterial Tcps
Cited by: 2
Author(s): Mohammed Alaidarous
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.3341

Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents
Cited by: 19
Author(s): Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M. Normi, Fairolniza Mohd Shariff, Thean Chor Leow
Software Mentions: 1
Published: about 9 years ago

10.7717/peerj.11215

Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq
Cited by: 8
Author(s): Claudia-Anahí Pérez-Torres, Enrique Ibarra-Laclette, Eric E. Hernández-Domínguez, Benjamín Rodríguez-Haas, Alan-Josué Pérez-Lira, Emanuel Villafán, Alexandro Alonso-Sánchez, Clemente de Jesús García-Ávila, José-Abrahán Ramírez-Pool, Diana Sánchez-Rangel
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7818

Bioinformatic and biochemical analysis of the key binding sites of the pheromone binding protein of Cyrtotrachelus buqueti Guerin-Meneville (Coleoptera: Curculionidea)
Cited by: 8
Author(s): Hua Yang, Yanlin Liu, Yuanyuan Tao, Wei Yang, Chunping Yang, Jing Zhang, Li-Zhi Qian, Hao Líu, Zhiyong Wang
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.5379

Genome-wide identification and characterization of non-specific lipid transfer proteins in cabbage
Cited by: 11
Author(s): Jialei Ji, Honghao Lv, Limei Yang, Zhiyuan Fang, Mu Zhuang, Yangyong Zhang, Yumei Liu, Zhansheng Li
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.4347

Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerantPseudomonassp. AMS8
Cited by: 11
Author(s): Lawal Garba, Mohamad Ariff Mohamad Yussoff, Khairul Bariyyah Abd Halim, Siti Nor Hasmah Ishak, Mohd Shukuri Mohamad Ali, Siti Nurbaya Oslan, Raja Noor Zaliha Raja Abd Rahman
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.2602

In silico study on anti-Chikungunya virus activity of hesperetin
Cited by: 27
Author(s): Adrian Oo, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly Abu Bakar, Keivan Zandi
Software Mentions: 1
Published: almost 10 years ago

10.7717/peerj.7329

Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study
Cited by: 9
Author(s): Changyu Shan, Hongwei Li, Yuping Zhang, Yuyan Li, Ying‐Chun Chen, He Wang
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.1344

ProCS15: a DFT-based chemical shift predictor for backbone and Cβatoms in proteins
Cited by: 13
Author(s): Anders S. Larsen, Lars Andersen Bratholm, Anders S. Christensen, Maher Jan Channir, Jan H. Jensen
Software Mentions: 1
Published: almost 11 years ago

10.7717/peerj.2286

Engineering a light-controlled F1ATPase using structure-based protein design
Cited by: 6
Author(s): Daniel Hoersch
Software Mentions: 1
Published: about 10 years ago

10.7717/peerj.679

Bacillus anthracispXO1 plasmid encodes a putative membrane-bound bacteriocin
Cited by: 1
Author(s): Agata P. Perlinska, Marcin Grynberg
Software Mentions: 1
Published: over 11 years ago

10.7717/peerj.9063

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress
Cited by: 14
Author(s): Yu Zang, Jun Chen, Ruoxi Li, Shuai Shang, Xuexi Tang
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.11951

Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR
Cited by: 10
Author(s): Suparna Ghosh, Seketoulie Keretsu, Seung Joo Cho
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.9855

Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2)
Cited by: 6
Author(s): Rajesh Anand, Subham Biswal, Renu Bhatt, Bhupendra N. Tiwary
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.10888

In silico characterization and homology modeling of cytosolic APX gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea
Cited by: 1
Author(s): Anshika Tyagi, Sandhya Sharma, Harsha Srivastava, Nagendra Singh, Kishor Gaikwad
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.861

Bayesian inference of protein structure from chemical shift data
Cited by: 11
Author(s): Lars Andersen Bratholm, Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen
Software Mentions: 1
Published: over 11 years ago

10.7717/peerj.2322

Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking
Cited by: 44
Author(s): Saw Simeon, Nuttapat Anuwongcharoen, Watshara Shoombuatong, Aijaz Ahmad Malik, Virapong Prachayasittikul, Jarl E. S. Wikberg, Chanin Nantasenamat
Software Mentions: 1
Published: about 10 years ago

10.7717/peerj.7425

Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics
Cited by: 5
Author(s): Garima Singh, Sri Krishna Jayadev Magani, R.C. Sharma, Basharat Ahmad Bhat, Ashish Shrivastava, Madhusudhan Chinthakindi, Ashutosh Singh
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.2136

Simple approach for ranking structure determining residues
Cited by: 2
Author(s): Oscar D. Luna-Martínez, Abraham Vidal-Limón, Miryam I. Villalba-Velázquez, Rosalba Sánchez-Alcalá, Ramón Garduño‐Juárez, Vladimir N. Uversky, Baltazar Becerril
Software Mentions: 1
Published: about 10 years ago

10.7717/peerj.798

Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease–substrate interactions
Cited by: 9
Author(s): Humberto Fernandes, Eoin N Leen, Hamlet Cromwell, Marc-Philipp Pfeil, Stephen Curry
Software Mentions: 1
Published: over 11 years ago

10.1007/s00424-014-1603-2

Two helices in the third intracellular loop determine anoctamin 1 (TMEM16A) activation by calcium
Cited by: 10
Author(s): Jesun Lee, James A. Jung, Min Ho Tak, Jungwon Wee, Byeongjoon Lee, Yongwoo Jang, Hyeyeon Chun, Dong‐Jin Yang, Young Soon Yang, Sang Ho Park, Byung Woo Han, Soonsil Hyun, Jaehoon Yu, Hawon Cho, H. Criss Hartzell, Uhtaek Oh
Software Mentions: 1
Published: almost 12 years ago

10.3390/ph14030241

Schisandrol A Suppresses Catabolic Factor Expression by Blocking NF-κB Signaling in Osteoarthritis
Cited by: 3
Author(s): Seong Jae Han, Jimoon Jun, Seong‐il Eyun, Choong-Gu Lee, Jimin Jeon, Cheol‐Ho Pan
Software Mentions: 1
Published: over 5 years ago

10.3390/ph8030455

On the Quest of Cellular Functions of PEA-15 and the Therapeutic Opportunities
Cited by: 8
Author(s): Yufeng Wei
Software Mentions: 1
Published: about 11 years ago

10.3390/ph14040357

Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis
Cited by: 20
Author(s): Magdi E. A. Zaki, Sami A. Al‐Hussain, Vijay H. Masand, Siddhartha Akasapu, Sumit O. Bajaj, Nahed N. E. El-Sayed, Arabinda Ghosh, Israa Lewaa
Software Mentions: 1
Published: over 5 years ago

10.3390/ph13120447

Inhibition of SARS-CoV-2 Entry into Host Cells Using Small Molecules
Cited by: 22
Author(s): Kenana Al Adem, Aya Shanti, Cesare Stefanini, Sungmun Lee
Software Mentions: 1
Published: over 5 years ago

10.3390/ph14070638

Novel Purine Chemotypes with Activity against Plasmodium falciparum and Trypanosoma cruzi
Cited by: 5
Author(s): Nieves Martínez-Peinado, Álvaro Lorente-Macías, Alejandro García-Salguero, Nuria Cortés-Serra, Ángel Fenollar-Collado, Albert Ros-Lucas, Joaquím Gascón, María Jesús Pinazo, Ignacio J. Molina, Asier Unciti‐Broceta, Juan José Díaz‐Mochón, María José Pineda de las Infantas y Villatoro, Luís Izquierdo, Julio Alonso-Padilla
Software Mentions: 1
Published: about 5 years ago

10.3390/ph14030265

Novel Selective IDO1 Inhibitors with Isoxazolo[5,4-d]pyrimidin-4(5H)-one Scaffold
Cited by: 4
Author(s): Ana Dolšak, Tomaž Bratkovič, Larisa Mlinarič, Eva Ogorevc, Urban Švajger, Stanislav Gobec, Matej Sova
Software Mentions: 1
Published: over 5 years ago

10.3390/ph13060118

Design and Development of Novel Urea, Sulfonyltriurea, and Sulfonamide Derivatives as Potential Inhibitors of Sphingosine Kinase 1
Cited by: 12
Author(s): Sonam Roy, Amarjyoti Das Mahapatra, Taj Mohammad, Preeti Gupta, Mohamed F. Alajmi, Afzal Hussain, Tabish Rehman, Bhaskar Datta, Md. Imtaiyaz Hassan
Software Mentions: 1
Published: about 6 years ago

10.3390/ph14060572

Antimicrobial Activity of a Library of Thioxanthones and Their Potential as Efflux Pump Inhibitors
Cited by: 10
Author(s): Fernando Durães, Andreia Palmeira, B. Nieves Cruz, Joana Freitas-Silva, Nikoletta Szemerédi, Luı́s Gales, Paulo Martins da Costa, Fernando Remião, Renata Silva, Madalena Pinto, Gabriella Spengler, Emı́lia Sousa
Software Mentions: 1
Published: about 5 years ago

10.3390/ph13100277

Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations
Cited by: 33
Author(s): Anastasiia I. Petushkova, Andrey A. Zamyatnin
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1003341

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison
Cited by: 36
Author(s): Janez Konc, Milan Hodošček, Mitja Ogrizek, Joanna Trykowska Konc, Dušanka Janežič
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1003545

Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers
Cited by: 24
Author(s): U ManChon, Eric Talevich, Samiksha Katiyar, Khaled Rasheed, Natarajan Kannan
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1003744

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
Cited by: 38
Author(s): Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff‐Larsen, Elena Papaleo
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1006237

Statistical investigations of protein residue direct couplings
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1000083

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
Cited by: 44
Author(s): Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luís Serrano, Frédéric Rousseau, Joost Schymkowitz
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pcbi.1003585

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors
Cited by: 59
Author(s): Lars Boukharta, Hugo Gutiérrez‐de‐Terán, Johan Åqvist
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pcbi.1005787

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
Cited by: 23
Author(s): Gudrun Gygli, Fátima Lucas, Vı́ctor Guallar, Willem J.H. van Berkel
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1002068

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
Cited by: 71
Author(s): Élodie Laine, Isaure Chauvot de Beauchêne, David Pérahia, Christian Auclair, Luba Tchertanov
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pcbi.1000484

Computation of Conformational Coupling in Allosteric Proteins
Cited by: 50
Author(s): Brian Kidd, David Baker, Wendy E. Thomas
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pcbi.1000441

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
Cited by: 90
Author(s): Lun Yang, Jian Chen, Lin He
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pcbi.1006511

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
Cited by: 23
Author(s): Ying‐Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing‐Ke Weng, Yi Wang
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pcbi.1007193

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
Cited by: 14
Author(s): Bogdan Barz, Jennifer Loschwitz, Birgit Strodel
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1002103

Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases
Cited by: 19
Author(s): Michael D. Daily, George N. Phillips, Qiang Cui
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pcbi.1006295

The permeation mechanism of organic cations through a CNG mimic channel
Cited by: 1
Author(s): L.M. Napolitano, Arin Marchesi, Álex Rodríguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pcbi.1002128

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex
Cited by: 28
Author(s): A. Sofia F. Oliveira, António M. Baptista, Cláudio M. Soares
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pcbi.1002754

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network
Cited by: 16
Author(s): Sjoerd J. L. van Wijk, Adrien Melquiond, Sjoerd J. de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pcbi.0020098

Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome
Cited by: 87
Author(s): Adrian H. Elcock
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pcbi.1002555

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Cited by: 84
Author(s): Yasuhiro Matsunaga, Hiroya Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1003718

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides
Cited by: 34
Author(s): James B. Smadbeck, Kiat Hwa Chan, George Khoury, Bin Xue, Robert Robinson, Charlotte Hauser, Christodoulos A. Floudas
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1000293

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
Cited by: 99
Author(s): Michael D. Daily, Jeffrey J. Gray
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.1004661

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
Cited by: 17
Author(s): Tatjana Braun, Julia Koehler Leman, Oliver Lange
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1000376

Prediction of Protein Binding Regions in Disordered Proteins
Cited by: 525
Author(s): Bálint Mészáros, István Simon, Zsuzsanna Dosztányi
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.1006969

A global map of the protein shape universe
Cited by: 19
Author(s): Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1002646

The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles
Cited by: 11
Author(s): Deena M.A. Gendoo, Paul M. Harrison
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1007569

Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
Cited by: 38
Author(s): Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1003253

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
Cited by: 55
Author(s): Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain Wallace, Vinod Kumar, Ursula Pieper, Andrej Šali, James R. Brown, John P. Overington, Marc A. Martí‐Renom
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1000689

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease
Cited by: 21
Author(s): Neema L. Salimi, Bosco Ho, David A. Agard
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1002509

Dynamic Prestress in a Globular Protein
Cited by: 28
Author(s): Scott A. Edwards, J. Wagner, Frauke Gräter
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1000360

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Cited by: 126
Author(s): Zheng Yang, Peter Marynen, İvet Bahar
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.1000668

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures
Cited by: 44
Author(s): Fred P. Davis, Andrej Šali
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1003249

Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
Cited by: 75
Author(s): Fan Jin, Yu Chen, Luhua Lai, Zhongfan Liu
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1002016

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study
Cited by: 92
Author(s): Lun Yang, Kejian Wang, Jian Chen, Anil G. Jegga, Heng Luo, Leming Shi, Chunling Wan, Xiaolei Guo, Shengying Qin, Guang He, Feng Gao, Lin He
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1004548

Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains
Cited by: 18
Author(s): Anja Winter, Ralf Schmid, Richard Bayliss
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1009009

Ten simple rules for designing analogue science games
Cited by: 1
Author(s): Sam Illingworth, Paul Wake
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1008818

Prediction of amphipathic helix—membrane interactions with Rosetta
Cited by: 3
Author(s): Alican Gulsevin, Jens Meiler
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1002682

Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
Cited by: 39
Author(s): Iskra Staneva, Yongqi Huang, Zhongfan Liu, Stefan Wallin
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pcbi.1006126

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin
Cited by: 15
Author(s): Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen
Software Mentions: 1
Published: over 8 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266