pypi: PyMOL | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pcbi.0030211

Detecting Coevolution in and among Protein Domains
Cited by: 157
Author(s): Chen Hsiang Yeang, David Haussler
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pcbi.1000056

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains
Cited by: 54
Author(s): Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.1003901

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
Cited by: 13
Author(s): Kei Moritsugu, Tohru Terada, Akinori Kidera
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1005826

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
Cited by: 17
Author(s): Shaima Hashem, Matteo Tiberti, Arianna Fornili
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1008403

Ten simple rules for starting research in your late teens
Cited by: 0
Author(s): Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1002869

Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore
Cited by: 65
Author(s): Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xianzhong Dai, Jianfeng Wang, Hongen Li, Xin Wang, Winson Jianhong Tan, Mingjing Luo, Xiaodi Niu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.0040043

Accurate Structural Correlations from Maximum Likelihood Superpositions
Cited by: 86
Author(s): Douglas L. Theobald, Deborah S. Wuttke
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.0020124

The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
Cited by: 107
Author(s): Wankyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pcbi.1002420

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB
Cited by: 35
Author(s): Elif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloğlu
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1000627

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
Cited by: 56
Author(s): Menachem Fromer, Julia M. Shifman
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1000406

A Probabilistic Model of RNA Conformational Space
Cited by: 83
Author(s): Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff‐Borg, Thomas Hamelryck
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pcbi.1008101

Quantitative profiling of protease specificity
Cited by: 5
Author(s): Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1006458

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling
Cited by: 52
Author(s): Tatu Pantsar, Sami Rissanen, Daniel Dauch, Tuomo Laitinen, Ilpo Vattulainen, Antti Poso
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pcbi.1007714

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex
Cited by: 11
Author(s): Dmitrii S. Shcherbinin, Vlad A. Belousov, Mikhail Shugay
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1003749

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
Cited by: 27
Author(s): Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Élodie Laine, Alain Trouvé, Patrice Dubreuil, Luba Tchertanov
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1002674

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
Cited by: 28
Author(s): Andrei V. Pisliakov, Tsuneo Hino, Yoshitsugu Shiro, Yuji Sugita
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pcbi.1000367

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)
Cited by: 26
Author(s): Srinivas Ramachandran, Adrian W.R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.1002929

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
Cited by: 46
Author(s): Pouria Dasmeh, Adrian W.R. Serohijos, Kasper Planeta Kepp, Eugene I. Shakhnovich
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1004282

Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2
Cited by: 20
Author(s): Juan A. Bueren-Calabuig, Julien Michel
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.1004556

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
Cited by: 132
Author(s): David Bednář, Koen Beerens, Eva Šebestová, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupková, Zbyněk Prokop, Jan Brezovský, David Baker, Jiřı́ Damborský
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1005948

The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
Cited by: 17
Author(s): Ravi Kumar Verma, Ara M. Abramyan, Mayako Michino, R. Benjamin Free, David R. Sibley, Jonathan A. Javitch, J. Robert Lane, Lei Shi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1000772

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences
Cited by: 92
Author(s): Vinal Lakhani, Feng Ding, Nikolay V. Dokholyan
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1004834

Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
Cited by: 18
Author(s): Sandhya Tiwari, Nathalie Reuter
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1001042

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation
Cited by: 20
Author(s): Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pgen.1007881

Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis
Cited by: 25
Author(s): Jia-Chi Ku, Arnaud Ronceret, Inna N. Golubovskaya, Ding Hua Lee, Rachel Wang, Ljudmilla Timofejeva, Yu-Hsin Kao, Ana Karen Gomez Angoa, Karl A. Kremling, Rosalind Williams‐Carrier, Robert B. Meeley, Alice Barkan, W. Zacheus Cande
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1008208

Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies
Cited by: 24
Author(s): Sook Wah Yee, Adrian Stecula, Huan‐Chieh Chien, Ling Zou, Elena V. Feofanova, Marjolein van Borselen, Kit Wun Kathy Cheung, Noha A. Yousri, Karsten Suhre, Jason M. Kinchen, Eric Boerwinkle, Roshanak Irannejad, Bing Yu, Kathleen M. Giacomini
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1004784

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response
Cited by: 122
Author(s): Erin Becker, Phillip Seitzer, Andrew Tritt, David Larsen, Megan L. Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling, Marc T. Facciotti
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1007009

Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model
Cited by: 21
Author(s): Edward B. Li, Dawn Truong, Shawn A Hallett, Kusumika Mukherjee, Brian C. Schutte, Eric C. Liao
Software Mentions: 1
Published: almost 9 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266